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| # | Question Report | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 |
|---|---|---|---|---|---|---|---|---|---|
| 1 | Report Generated: | 2023-04-21 16:31:00 | 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 | 2023-04-20 14:30:00 | 119 | 25 | 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 | is there any sample code for lab session today? | dhe2 | '- | Yes, it’s in github as usual. | 2023-04-20 15:05:00 | 2023-04-20 15:05:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 7 | 2 | is it recording? | Yanghyeon Cho | '- | Yes, we’ll provide a link later. | 2023-04-20 15:08:00 | 2023-04-20 15:09:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 8 | 3 | there are 4 files in lecture 4, none seems to be a R code | dhe2 | '- | The html files have the R code. | 2023-04-20 15:09:00 | 2023-04-20 15:10:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 9 | 3 | there are 4 files in lecture 4, none seems to be a R code | dhe2 | '- | Download the files and open in a browser to see the code. | 2023-04-20 15:09:00 | 2023-04-20 15:10:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 10 | 4 | got it, thanks | dhe2 | '- | nan | 2023-04-20 15:10:00 | nan | nan | nan |
| 11 | 5 | In slide 9, can we estimate beta(M,j) of the model when p is slightly greather than the N? | Hyunkyu Lee | '- | Yes, that’s where variable selection is needed as you see in later slides. | 2023-04-20 15:15:00 | 2023-04-20 15:20:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 12 | 6 | is there a reference for methods in slide 14? | Joanne TY Lim | '- | The results from Slide #14 are from the lab session. Rick will go over those in the lab. The methods are from HIMA (slide 13). | 2023-04-20 15:25:00 | 2023-04-20 15:29:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 13 | 7 | This might be a bit of general question - how do you compute the 1 year survival outcome? Do you use overall survival? Please expand abit about this? how do you deal with censor data? | Anonymous Attendee | nan | We dichotomize the survival and remove censoring cases that are not sure for simplicity. This is only for demonstration purpose. | 2023-04-20 15:25:00 | 2023-04-20 15:33:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 14 | 8 | This model seems very similar to mendelian randomization. When theta is non-zero, how do we separate the proportion of alpha and theta? | Hyunkyu Lee | '- | theta is the direct effect, while alpha times beta is the indirect effect. The proportion of mediation effect is alpha*beta/gamma where gamma is fitting effect without any mediators. | 2023-04-20 15:25:00 | 2023-04-20 15:41:00 | Wenjia Wang | wew89@pitt.edu |
| 15 | 8 | This model seems very similar to mendelian randomization. When theta is non-zero, how do we separate the proportion of alpha and theta? | Hyunkyu Lee | '- | Also, here is a recent reference if you want to learn more about the differences: https://link.springer.com/article/10.1007/s10654-021-00757-1 | 2023-04-20 15:25:00 | 2023-04-20 15:42:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 16 | 9 | In slide 13, can we still process to next step if d is still greater than sample size after SIS? | xiqiao | '- | You’ll see in the lab that d is selected to be n/(2*logn). | 2023-04-20 15:26:00 | 2023-04-20 15:33:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 17 | 9 | In slide 13, can we still process to next step if d is still greater than sample size after SIS? | xiqiao | '- | You can define the top d where d<n. Refer to Fan, J. and Lv, J. (2008), Sure independence screening for ultrahigh dimensional feature space. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 70: 849-911. https://doi.org/10.1111/j.1467-9868.2008.00674.x for details. | 2023-04-20 15:26:00 | 2023-04-20 15:34:00 | Wenjia Wang | wew89@pitt.edu |
| 18 | 10 | For clusting or causal relationship analyses, what type of data is preferred? 1.sc data from a single sample 2. sc data from multiple different samples. | Hyunkyu Lee | '- | Generally, the sc dataset is from one sample. In order to enlarge the data size, you can use multiple sc data sets from multiple samples, but you need to first integrate them to matching and batch correction. | 2023-04-20 15:41:00 | 2023-04-20 15:44:00 | Wenjia Wang | wew89@pitt.edu |
| 19 | 11 | Thanks. is the overfitting issue with sc data from a single sample normally negligible? | Hyunkyu Lee | '- | Sample size is different here in that there are 100-1000s of cells for the sample and many cells of each cell type. | 2023-04-20 15:46:00 | 2023-04-20 15:48:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 20 | 12 | I don’t seem able to open the lab at all. The html file does not open for me | Anonymous Attendee | nan | Click on the html file in GitHub, then click on the raw and you’ll get the raw html code. Then you can download this file and open it in a browser. | 2023-04-20 15:58:00 | 2023-04-20 16:00:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 21 | 12 | I don’t seem able to open the lab at all. The html file does not open for me | Anonymous Attendee | nan | In my case, if I click “view raw” or “download”, my browser gave strange thing. I right clicked on “View Raw” and used “Download Linked File as”. That will allow you to save the html file. | 2023-04-20 15:58:00 | 2023-04-20 16:06:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 22 | 13 | What exactly does “5% mediation effect” mean? | Monnie McGee | '- | It quantifies the percent of varaition explained by mediation effect. Similar to the concept of R^2 in regression. | 2023-04-20 16:03:00 | 2023-04-20 16:07:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 23 | 14 | Is mediation analysis mathematically the same as generalized SEM? Can HIMA model multiple outcomes or mediators with different distributions? | Hossein Asgharian | '- | Structural Equation Modeling (SEM) is a broader framework to multivariable analysis exploring relationships between variables. SEM is a tool for mediation analysis. | 2023-04-20 16:04:00 | 2023-04-20 16:09:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 24 | 14 | Is mediation analysis mathematically the same as generalized SEM? Can HIMA model multiple outcomes or mediators with different distributions? | Hossein Asgharian | '- | HIMA’s paper does not work for multiple outcomes. | 2023-04-20 16:04:00 | 2023-04-20 16:09:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 25 | 14 | Is mediation analysis mathematically the same as generalized SEM? Can HIMA model multiple outcomes or mediators with different distributions? | Hossein Asgharian | '- | Here are a reference for more reading: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054581/ | 2023-04-20 16:04:00 | 2023-04-20 16:10:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 26 | 15 | > cite <- FindNeighbors(cite, dims = 1:30, reduction = 'pca') Computing nearest neighbor graph Computing SNN Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found | dhe2 | '- | You can try to update your 'Matrix' package to 1.5.3 version to follow up with the nearest version of Seurat. | 2023-04-20 16:09:00 | 2023-04-20 16:13:00 | Wenjia Wang | wew89@pitt.edu |
| 27 | 15 | > cite <- FindNeighbors(cite, dims = 1:30, reduction = 'pca') Computing nearest neighbor graph Computing SNN Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found | dhe2 | '- | I also tested in Chrome and it worked. | 2023-04-20 16:09:00 | 2023-04-20 16:15:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 28 | 16 | who can explain this error?thanks | dhe2 | '- | nan | 2023-04-20 16:10:00 | nan | nan | nan |
| 29 | 17 | I have cloned the github folder on my computer. But i still cannot open the html file. I get “safari can’t open the Page” will the R script use to generate the report be made available? | Anonymous Attendee | nan | You can try to open it with chrome browser | 2023-04-20 16:13:00 | 2023-04-20 16:14:00 | Wenjia Wang | wew89@pitt.edu |
| 30 | 17 | I have cloned the github folder on my computer. But i still cannot open the html file. I get “safari can’t open the Page” will the R script use to generate the report be made available? | Anonymous Attendee | nan | I also tested in Chrome and it worked. After clicking on raw version in GitHub, use download button at the right of the link text which will save locally and then you can click on that file after you downloaded and open in Chrome. | 2023-04-20 16:13:00 | 2023-04-20 16:16:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 31 | 18 | ok, will try | dhe2 | '- | nan | 2023-04-20 16:14:00 | nan | nan | nan |
| 32 | 19 | haha! that works. | Anonymous Attendee | nan | nan | 2023-04-20 16:18:00 | nan | nan | nan |
| 33 | 20 | Will the recordings expire at some point? | Manni Zhang | '- | They are on YouTube and shouldn’t expire. They are on a special section channel and are not searchable, but you will have the link and password. | 2023-04-20 16:19:00 | 2023-04-20 16:22:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 34 | 21 | Is there annual fee for ASA SSGG membership? | Anonymous Attendee | nan | https://www.amstat.org/membership/become-a-member/membership-options | 2023-04-20 16:22:00 | 2023-04-20 16:23:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 35 | 22 | For people from industry?? | Anonymous Attendee | nan | https://www.amstat.org/membership/become-a-member/membership-options | 2023-04-20 16:22:00 | 2023-04-20 16:23:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 36 | 23 | Got it - thank you! | Anonymous Attendee | nan | nan | 2023-04-20 16:23:00 | nan | nan | nan |
| 37 | 24 | The r script for today’s lecture/lab will be available? | Anonymous Attendee | nan | Please see GitHub folder for lecture 4 | 2023-04-20 16:24:00 | 2023-04-20 16:24:00 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 38 | 24 | The r script for today’s lecture/lab will be available? | Anonymous Attendee | nan | https://github.com/KechrisLab/ASAShortCourse-MultiOmics/tree/main/Lecture%204 | 2023-04-20 16:24:00 | 2023-04-20 16:25:00 | Rick Chang | rick.chang@pitt.edu |
| 39 | 25 | Sorry this is an afterthought - Any suggestions on how we can better integrate GWAS data/PRS scores into these analyses? | Joanne TY Lim | '- | nan | 2023-04-20 16:25:00 | nan | nan | nan |