Datasets
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| 1 | Report Generated: | 45027.700694444444 | nan | nan | nan | nan | nan | nan | nan |
| 2 | Topic | Webinar ID | Actual Start Time | Actual Duration (minutes) | # Question | nan | nan | nan | nan |
| 3 | ASA-SSGG Short Course Series: Selective Introduction to Multi-Omics Analysis | 950 5160 1391 | 45027.60138888889 | 142 | 59 | nan | nan | nan | nan |
| 4 | Question Details | nan | nan | nan | nan | nan | nan | nan | nan |
| 5 | # | Question | Asker Name | Asker Email | Answer | Question Time | Answered Time | Answer Name | Answer Email |
| 6 | 1 | Hello | Yab | '- | nan | 45027.62530092592 | nan | nan | nan |
| 7 | 2 | Test | Xuewei Cao | '- | nan | 45027.6253125 | nan | nan | nan |
| 8 | 3 | working? | Jennifer Bryant | '- | nan | 45027.6253125 | nan | nan | nan |
| 9 | 4 | This is a test. | [NBI] Florian Prodinger | '- | nan | 45027.62532407408 | nan | nan | nan |
| 10 | 5 | Hello | Jenea I. Adams | '- | nan | 45027.62533564815 | nan | nan | nan |
| 11 | 6 | Test | Emily Isenhart | '- | nan | 45027.62533564815 | nan | nan | nan |
| 12 | 7 | test | Joanne TY Lim | '- | nan | 45027.62533564815 | nan | nan | nan |
| 13 | 8 | hi | Anna Giczewska | '- | nan | 45027.62533564815 | nan | nan | nan |
| 14 | 9 | Hi | Ruohan Liao | '- | nan | 45027.62538194445 | nan | nan | nan |
| 15 | 10 | Test | Jun | '- | nan | 45027.62538194445 | nan | nan | nan |
| 16 | 11 | test | Hyunkyu Lee | '- | nan | 45027.62954861111 | nan | nan | nan |
| 17 | 12 | Where are the needed packages listed? | adelle.price@ucdenver.edu | '- | https://github.com/KechrisLab/ASAShortCourse-MultiOmics | 45027.63041666667 | 45027.630694444444 | Jack Pattee | jack.pattee@cuanschutz.edu |
| 18 | 13 | can we fork this? | Kazi Tanvir Hasan | '- | live answered | 45027.63190972222 | 45027.633784722224 | Jack Pattee | jack.pattee@cuanschutz.edu |
| 19 | 13 | can we fork this? | Kazi Tanvir Hasan | '- | Sure. | 45027.63190972222 | 45027.63390046296 | Jack Pattee | jack.pattee@cuanschutz.edu |
| 20 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | if you use docker, you don’t need to install packages. That container has included all the packages you need. Let me know if you are unable to install docker | 45027.63321759259 | 45027.63674768519 | Rick Chang | rick.chang@pitt.edu |
| 21 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | How the docker be used in R? | 45027.63321759259 | 45027.63715277778 | Neng Wang | '- |
| 22 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | we don’t use docker in R. They are two different application. You can use docker on terminal | 45027.63321759259 | 45027.637974537036 | Rick Chang | rick.chang@pitt.edu |
| 23 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | Is there a tourial for how to use docker on terminal? | 45027.63321759259 | 45027.63893518518 | Neng Wang | '- |
| 24 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | Yes. its on github https://github.com/KechrisLab/ASAShortCourse-MultiOmics/tree/main/Lecture%201 | 45027.63321759259 | 45027.639699074076 | Rick Chang | rick.chang@pitt.edu |
| 25 | 14 | I read your tutorial of metaomics, it seems out of service. current > R.4.0 can not install packages, while R 3.3 neither. even i can not install in your docker container. really frustrating and hope you can help. | gwu | '- | by following steps 1) Install docker: https://www.docker.com/ 2) Run command in terminal: - docker pull metaomics/app - docker run --rm --name metaOmics -p 3838:3838 metaomics/app | 45027.63321759259 | 45027.640543981484 | Rick Chang | rick.chang@pitt.edu |
| 26 | 15 | Will we be able to download the slides? | Jennifer Bryant | '- | Yes, we will post the slides on the GitHub site. | 45027.637141203704 | 45027.637974537036 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 27 | 15 | Will we be able to download the slides? | Jennifer Bryant | '- | Great, thank you! | 45027.637141203704 | 45027.638287037036 | Jennifer Bryant | '- |
| 28 | 15 | Will we be able to download the slides? | Jennifer Bryant | '- | Also forgot to mention that this Lecture is already posted, see Lecture1 folder on GitHub, | 45027.637141203704 | 45027.63872685185 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 29 | 16 | Dr. Tseng mentioned experimental design as part of the data analysis process (slide 13). Can you point me to information on experimental design for these types of experiments? This seems like an area that is largely ignored. | Monnie McGee | '- | This is a vast topic and can be technology specific (sequencing, mass spectrometry, etc). Sampling aspects follow principles of experimental desgin - not necessarily omics specific. If anyone else is interested, I can follow up separately with references. | 45027.63890046296 | 45027.641863425924 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 30 | 17 | I follow the instruction to install docker and run some commands, but I recieve this warning message “WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested” | Anonymous Attendee | nan | no worries. arm64 and amd64 are two different machine architecture. it wouldn’t affect the analysis result | 45027.64013888889 | 45027.64320601852 | Rick Chang | rick.chang@pitt.edu |
| 31 | 18 | I got the same warning but the web app seems to still work | Tim Vigers (he/him) | '- | yes! thanks for helping to answer the question!!! | 45027.6412037037 | 45027.64351851852 | Rick Chang | rick.chang@pitt.edu |
| 32 | 19 | Will we cover methods to deal with missing data (partial matching of samples) and different levels of noisiness across data types? | Hossein Asgharian | '- | With my lecture on Thursday, we will mention that most methods require no missing data but can use imputation (such as KNN), prior to analysis if needed. For the specific method we’ll highlight (similarity network fusion), we will also show how it can address noisiness/data heterogenity across data types. | 45027.64131944445 | 45027.64324074074 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 33 | 19 | Will we cover methods to deal with missing data (partial matching of samples) and different levels of noisiness across data types? | Hossein Asgharian | '- | However, we won’t go into great depth on this topic due to the limited time we have in this short course. Feel free to email us if you’d like specific references. | 45027.64131944445 | 45027.64430555556 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 34 | 19 | Will we cover methods to deal with missing data (partial matching of samples) and different levels of noisiness across data types? | Hossein Asgharian | '- | This is a good question. How to deal with partially matched data is understudied and not easy. Most people simply drop partial data. My lab has two papers. You may find other references from there if interested. Zhou Fang, Tianzhou Ma, Gong Tang, Li Zhu, Qi Yan, Ting Wang, Juan C. Celedon, Wei Chen* and George C. Tseng*. (2018) Bayesian integrative model for multi-omics data with missingness. Bioinformatics. 34:3801-3808. Mingling Gong, Peng Liu, Frank C. Sciurba, Petar Stojanov, Dacheng Tao, George C. Tseng, Kun Zhang, Kayhan Batmanghelich. (2021) Unpaired Data Empowers Association Tests. Bioinformatics. 37:785-792. | 45027.64131944445 | 45027.65244212963 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 35 | 20 | QUICK AUESTION: IN MetaOmics, how to quantify the batch effect across different platform? | gwu | '- | Meta-analysis combine signal/effect sizes so it is less impacted by batch effect. An alternative approach is to normalize multiple cohorts and then perform a “mega-analysis”. In the case, batch effect has to be carefully examined in the normalization. | 45027.652592592596 | 45027.654328703706 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 36 | 20 | QUICK AUESTION: IN MetaOmics, how to quantify the batch effect across different platform? | gwu | '- | A related answer to this. MetaOmics has a package called MetaQC. The purpose is not for batch effect but for detecting studies of problematic quality. Users can then more objectively exclude low-quality studies. Dongwan D. Kang, Etienne Sibille, Naftali Kaminski, and George C. Tseng*. (2012) MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis. Nucleic Acids Research. 40(2):e15. | 45027.652592592596 | 45027.65641203704 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 37 | 21 | If the sample sizes are very different, how does that effect the accuracy/precision/performance of MetaNetwork? For example, does study 3 on page 29 have fewer subjects or is it the technology that results in fewer connections in the network (and thus a smaller correlation). | Monnie McGee | '- | Smaller sample size generates less stable correlation measure but not necessarily smaller. Indeed, the current MetaNetwork method does not consider sample size effect. But if a strong differential network is detected across multiple studies, it’ll be a reliable signal even small sample size in some studies. | 45027.656747685185 | 45027.65914351852 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 38 | 22 | I see. the effect sizes and significances were integrated in meta analysis. It is enough for differential analysis. do we need to consider batch effect in sample seperation? | gwu | '- | Take meta-analysis of DE analysis as an example, batch effect is not an issue since the p-values or effect sizes + variances are calculated in each cohort separately. It is only when we attempt to normalize all cohorts into one cohort to perform analysis (often called mega-analysis), we need to exampline batch effect. | 45027.65837962963 | 45027.66186342593 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 39 | 22 | I see. the effect sizes and significances were integrated in meta analysis. It is enough for differential analysis. do we need to consider batch effect in sample seperation? | gwu | '- | in your MetaClust, you mentioned sample cluster. are they still immune to batch effect? | 45027.65837962963 | 45027.664351851854 | gwu | '- |
| 40 | 22 | I see. the effect sizes and significances were integrated in meta analysis. It is enough for differential analysis. do we need to consider batch effect in sample seperation? | gwu | '- | That’s a good question. And the answer is yes. The method does not attempt to harmonize samples from multiple cohorts into one cohort and the design allows batch effect. | 45027.65837962963 | 45027.667708333334 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 41 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | did you get the following messages on terminal after “docker run”? [2023-04-11T16:20:26.771] [INFO] shiny-server - Shiny Server v1.5.7.890 (Node.js v8.10.0) [2023-04-11T16:20:26.776] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf" [2023-04-11T16:20:26.830] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root. [2023-04-11T16:20:26.833] [INFO] shiny-server - Starting listener on 0.0.0.0:3838 [2023-04-11T16:20:45.378] [INFO] shiny-server - Created bookmark state directory: /var/lib/shiny-server/bookmarks [2023-04-11T16:20:45.379] [INFO] shiny-server - Created user bookmark state directory: /var/lib/shiny-server/bookmarks/shiny | 45027.66063657407 | 45027.661828703705 | Rick Chang | rick.chang@pitt.edu |
| 42 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | Can you post yours here? Then I can check what happened. | 45027.66063657407 | 45027.66261574074 | Rick Chang | rick.chang@pitt.edu |
| 43 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | I have first to run docker before going to the site? | 45027.66063657407 | 45027.6628125 | Maria A Sans-Fuentes | '- |
| 44 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | Yes | 45027.66063657407 | 45027.66292824074 | Rick Chang | rick.chang@pitt.edu |
| 45 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | by following steps 1) Install docker: https://www.docker.com/ 2) Run command in terminal: docker pull metaomics/app docker run --rm --name metaOmics -p 3838:3838 metaomics/app | 45027.66063657407 | 45027.66322916667 | Rick Chang | rick.chang@pitt.edu |
| 46 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | Ok! now I could connect! thanks! | 45027.66063657407 | 45027.66333333333 | Maria A Sans-Fuentes | '- |
| 47 | 23 | I am trying to access to http://127.0.0.1:3838/metaOmics/, but the browser cannot connect to the server | Maria A Sans-Fuentes | '- | Np | 45027.66063657407 | 45027.663460648146 | Rick Chang | rick.chang@pitt.edu |
| 48 | 24 | Did metaclust consider overlapping modules? | Xuewei Cao | '- | Do you mean overlapping clusters? | 45027.66068287037 | 45027.66195601852 | Wenjia Wang | wew89@pitt.edu |
| 49 | 24 | Did metaclust consider overlapping modules? | Xuewei Cao | '- | Yes. Some genes may be clustered into difference modules. | 45027.66068287037 | 45027.66241898148 | Xuewei Cao | '- |
| 50 | 24 | Did metaclust consider overlapping modules? | Xuewei Cao | '- | MetaClust is to cluster samples into disease subtypes in multiple cohorts. It does not cluster genes into modules. | 45027.66068287037 | 45027.66284722222 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 51 | 25 | Got it. Thank you so much for your response. | Xuewei Cao | '- | nan | 45027.663449074076 | nan | nan | nan |
| 52 | 26 | Running MetaOmics in docker is a temporary solution. How can I run it in ordinary working environment in R > 4.1 | gwu | '- | It is unfortunately an issue for almost all R and shiny packages. Docker is designed to ensure that the environment and analysis are always feasible and reproducible after many years. If anyone has knowledge of a better solution, I would be glad to hear. | 45027.66688657407 | 45027.66981481481 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 53 | 26 | Running MetaOmics in docker is a temporary solution. How can I run it in ordinary working environment in R > 4.1 | gwu | '- | I see. the interface is through shiny in your website. It allows real data input and analysis. Thanks! | 45027.66688657407 | 45027.67568287037 | gwu | '- |
| 54 | 27 | When I try to read the file, it give me a message saying Disconnected from the server | Maria A Sans-Fuentes | '- | just reload the web browser | 45027.669444444444 | 45027.66987268518 | Rick Chang | rick.chang@pitt.edu |
| 55 | 28 | I did and it keep giving me the same message | Maria A Sans-Fuentes | '- | the other solution is 1) go to terminal and disconnect the docker (control + C) 2) re-run the command “”docker run | 45027.67018518518 | 45027.67178240741 | Rick Chang | rick.chang@pitt.edu |
| 56 | 29 | When trying to merge, it says subscript out of bounds | Dan Guzman | '- | Same here | 45027.6703125 | 45027.67049768518 | Wenjing Ma | '- |
| 57 | 29 | When trying to merge, it says subscript out of bounds | Dan Guzman | '- | sometimes it would happen. just reload the web browser and delete the file you uploaded. Then re-upload the file again | 45027.6703125 | 45027.67251157408 | Rick Chang | rick.chang@pitt.edu |
| 58 | 30 | too fast.....cannot follow | Daheng He | '- | Github has detailed tutorial to reproduce after lecture. Sorry that we’re limited by time and cannot troubleshoot or interact like an in-person lab session. | 45027.670949074076 | 45027.67267361111 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 59 | 30 | too fast.....cannot follow | Daheng He | '- | “MetaOmics_Tutorial.pdf” in Github. | 45027.670949074076 | 45027.67471064815 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 60 | 31 | Is there anyway we can pause to troubleshoot for people who are having trouble? | Dan Guzman | '- | Github has detailed tutorial to reproduce after lecture. Sorry that we’re limited by time and cannot troubleshoot or interact like an in-person lab session. | 45027.67109953704 | 45027.672743055555 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 61 | 31 | Is there anyway we can pause to troubleshoot for people who are having trouble? | Dan Guzman | '- | “MetaOmics_Tutorial.pdf” in Github. | 45027.67109953704 | 45027.67476851852 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 62 | 32 | why top 80% has less features than 50%? | Manni Zhang | '- | It is to filter 80% and leave 20% | 45027.6712962963 | 45027.672997685186 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 63 | 33 | cannot follow, this is way too fast | Daheng He | '- | nan | 45027.67207175926 | nan | nan | nan |
| 64 | 34 | Now I keep getting disconnected from the server when trying to go to MetaDE | Dan Guzman | '- | I am having the same issue | 45027.67246527778 | 45027.67303240741 | Spencer Woody | '- |
| 65 | 34 | Now I keep getting disconnected from the server when trying to go to MetaDE | Dan Guzman | '- | one quick solution is reload the browser. the other solution is 1) go to terminal and disconnect the docker (control + C) 2) re-run the command ”docker run” | 45027.67246527778 | 45027.673796296294 | Rick Chang | rick.chang@pitt.edu |
| 66 | 34 | Now I keep getting disconnected from the server when trying to go to MetaDE | Dan Guzman | '- | Even after restarting several times, when I select something from the tools menu, I get a server disconnect. | 45027.67246527778 | 45027.67837962963 | Randy Johnson | '- |
| 67 | 34 | Now I keep getting disconnected from the server when trying to go to MetaDE | Dan Guzman | '- | Same here | 45027.67246527778 | 45027.68035879629 | Dan Guzman | '- |
| 68 | 35 | Still the same :-( | Maria A Sans-Fuentes | '- | how about you show me the warning or error message after the lab session? Without seeing the warning messages, I don’t know what is going on. Thanks! | 45027.67375 | 45027.67649305556 | Rick Chang | rick.chang@pitt.edu |
| 69 | 36 | This is all based on R3.3, this means all the packages are also the versions from several years ago, right? Is your lab planning on updating this analysis suite to R4? | [NBI] Florian Prodinger | '- | We don’t have the manpower to maintain versions like a commercial software. Docker is the best solution we can find now. For statisticians, all packages and example codes are open source. Usually you only work on one of the packages (for example, MetaDE) and the debugging is more doable. | 45027.673784722225 | 45027.676875 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 70 | 36 | This is all based on R3.3, this means all the packages are also the versions from several years ago, right? Is your lab planning on updating this analysis suite to R4? | [NBI] Florian Prodinger | '- | thank you! | 45027.673784722225 | 45027.67884259259 | [NBI] Florian Prodinger | '- |
| 71 | 37 | I may have missed it, but were these raw count inputs for the three studies or normalized somehow (eg log-cpm, etc)? | Ryan Christian Augustin | '- | The example her is from old microrray with continuous values. | 45027.67506944444 | 45027.677303240744 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 72 | 38 | is there a recommended way to combine data generated using microarray and RNAseq? Can them be transformed into the same space? how about the 1 to many mapping relation between probesets in microarray and gene symbol in RNAseq | wei.x.3 | '- | The package has preprocessing routines to handle 1 to many mappings. The package can process both microarray and RNA-seq to continuous measurements for analysis. | 45027.67511574074 | 45027.678125 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 73 | 38 | is there a recommended way to combine data generated using microarray and RNAseq? Can them be transformed into the same space? how about the 1 to many mapping relation between probesets in microarray and gene symbol in RNAseq | wei.x.3 | '- | We did have a paper to combine microarray and RNA-seq. It gains some power/efficiency but statistical model and computing are a lot more demanding. Tianzhou Ma, Faming Liang, Steffi Oesterreich and George C. Tseng*. (2017) A joint Bayesian modeling for integrating microarray and RNA-seq transcriptomic data. Journal of Computational Biology. 24:647-662. | 45027.67511574074 | 45027.67940972222 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 74 | 39 | When I tried to plot heatmap, error message "replacement has length zero" even though I have 134 genes for plotting. Any suggestions? | Jiexin Zhang | '- | did you upload the clinical data? | 45027.67517361111 | 45027.67759259259 | Rick Chang | rick.chang@pitt.edu |
| 75 | 39 | When I tried to plot heatmap, error message "replacement has length zero" even though I have 134 genes for plotting. Any suggestions? | Jiexin Zhang | '- | Did you solve this problem? | 45027.67517361111 | 45027.68869212963 | Rick Chang | rick.chang@pitt.edu |
| 76 | 40 | is Kolmogorov vs. Fisher here essentially the same as GSEA vs. ORA? | Tim Vigers (he/him) | '- | Yes. | 45027.67569444444 | 45027.67824074074 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 77 | 41 | Pathway enrichment is really finnicky in my experience. How can we read out the parameters used for calculating the enrichment of pathways? | [NBI] Florian Prodinger | '- | The package adopts some standard pathway enrichment method. There’re areas to modify parameters of these methods but we recommend not to change unless users are familiar. | 45027.67591435185 | 45027.6805787037 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 78 | 42 | Ok! | Maria A Sans-Fuentes | '- | nan | 45027.678622685184 | nan | nan | nan |
| 79 | 43 | I am still trying to install docker. I am on an iMac running OS 12.6.2. When I open the docker desktop and click “Finish” to set up docker with recommended settings, I get “error invoking remote method ‘desktio-go-backend’: Error:{“message”:”applescript error 1049:1052: execution error: Error installing vmnnetd: retreiving vmnetd version from /Library/LaunchDaemons/com.docker.vmnetd. reading plist. It’s a really long error message - there is more. | Monnie McGee | '- | If you stay one, we can try to help you. | 45027.679247685184 | 45027.68714120371 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 80 | 44 | BTW - I started trying the install this morning. It wasn’t like I was waiting until the last minute. | Monnie McGee | '- | nan | 45027.67980324074 | nan | nan | nan |
| 81 | 45 | I think so. but in the saved data, only shows study1.csv and study2.csv, not the study_label files | Jiexin Zhang | '- | You may want to refresh the GitHub, the study#.label files should be in the Leukemia_Data directory. | 45027.67990740741 | 45027.68152777778 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 82 | 45 | I think so. but in the saved data, only shows study1.csv and study2.csv, not the study_label files | Jiexin Zhang | '- | Correct! Metaomics would combine study.csv with study_label files in the saved data. Let me figure out what is going on | 45027.67990740741 | 45027.68247685185 | Rick Chang | rick.chang@pitt.edu |
| 83 | 46 | Got it. Thanks. | Jiexin Zhang | '- | nan | 45027.68243055556 | nan | nan | nan |
| 84 | 47 | Does MetaOmics allow parallel computation for those computionally intensive tasks? | Anonymous Attendee | nan | yes. | 45027.68420138889 | 45027.68636574074 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 85 | 48 | Thank you for introducing this software suite today! | [NBI] Florian Prodinger | '- | nan | 45027.68445601852 | nan | nan | nan |
| 86 | 49 | Would you be able to elaborate more on how we should treat batch effects on these datasets? | Joanne TY Lim | '- | For metaDE analysis, you can choose p-value combination method (e.g. AWFisher), it is relative robust for batch effect. | 45027.684641203705 | 45027.69170138889 | Wenjia Wang | wew89@pitt.edu |
| 87 | 50 | are we able to see the Q&A when the recording is available? | Manni Zhang | '- | I don’t think so. But we’ll find a way to keep Q&A. | 45027.685069444444 | 45027.688055555554 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 88 | 51 | Hi, I couldn’t save the csv file from the github in a correct way. Could you please guide on this? thanks! | Anonymous Attendee | nan | I think you can directly type git clone https://github.com/KechrisLab/ASAShortCourse-MultiOmics.git | 45027.68547453704 | 45027.689791666664 | Wenjia Wang | wew89@pitt.edu |
| 89 | 51 | Hi, I couldn’t save the csv file from the github in a correct way. Could you please guide on this? thanks! | Anonymous Attendee | nan | or try to download the zip file | 45027.68547453704 | 45027.69032407407 | Rick Chang | rick.chang@pitt.edu |
| 90 | 51 | Hi, I couldn’t save the csv file from the github in a correct way. Could you please guide on this? thanks! | Anonymous Attendee | nan | go to GitHub and click “code” -> “download ZIP” | 45027.68547453704 | 45027.69143518519 | Rick Chang | rick.chang@pitt.edu |
| 91 | 52 | Can I download the recorded letures as well? | Yanghyeon Cho | '- | Yes, they will be posted at the ASA SSGG website. | 45027.68619212963 | 45027.68677083333 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 92 | 52 | Can I download the recorded letures as well? | Yanghyeon Cho | '- | Thanks! | 45027.68619212963 | 45027.6875462963 | Yanghyeon Cho | '- |
| 93 | 53 | What version of R will the MOVICS package work with, do you know? | Jennifer Bryant | '- | I’ve tried with the most current version (4.3.2), but it worked with some previous version as well. | 45027.68866898148 | 45027.68916666666 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 94 | 53 | What version of R will the MOVICS package work with, do you know? | Jennifer Bryant | '- | It also worked with the version prior to that. | 45027.68866898148 | 45027.68974537037 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 95 | 54 | Thanks | Subrata Paul | '- | nan | 45027.688680555555 | nan | nan | nan |
| 96 | 55 | Thank you! | Jiexin Zhang | '- | nan | 45027.68875 | nan | nan | nan |
| 97 | 56 | I'm getting an error message, package 'MOVICS' is not available for this version of R (4.2.3) | Jennifer Bryant | '- | Let me look into that. | 45027.68994212963 | 45027.69017361111 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 98 | 56 | I'm getting an error message, package 'MOVICS' is not available for this version of R (4.2.3) | Jennifer Bryant | '- | What command did you use? Try: devtools::install_github("xlucpu/MOVICS") | 45027.68994212963 | 45027.691342592596 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 99 | 57 | If I'm not admin on my machine, can I not install packages? | Jennifer Bryant | '- | Some of the packages may have issues with that, yes. | 45027.69020833333 | 45027.690520833334 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 100 | 58 | I have used R on a Mac (my own machine) and now have a windows machine that belongs to my employer - I have limited rights on the machine in terms of installing software and whatnot. I can try it on my personal machine and see if that works... | Jennifer Bryant | '- | Hmm… perhaps you can try it out and reach out if there are some issues. I can try to brainstorm ideas/solutions. | 45027.69087962963 | 45027.69248842593 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |