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| # | Question Report | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 |
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| 1 | Report Generated: | 2023-04-14 15:52:00 | 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 | 2023-04-13 14:15:00 | 150 | 42 | 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 | Hi there - I am struggling to install the MOVICS package and I'm wondering if I am lacking some dependencies - I've added testthat, knitr, rmarkdown, and kableExtra, are there others that I need to install? | Jennifer Bryant | '- | nan | 2023-04-13 14:24:22 | nan | nan | nan |
| 7 | 2 | I got the following error whenever I try to downlond “CIMLR” packages. ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [CIMLR.so] Error 1 ERROR: compilation failed for package ‘CIMLR’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/CIMLR’ Warning message: In i.p(...) : installation of package ‘/var/folders/t4/cdb0fwxs7z117qqykst9gsnm0000gn/T//RtmpDO43VK/file1554be49d93/CIMLR_1.0.0.tar.gz’ had non-zero exit status | Anonymous Attendee | nan | live answered | 2023-04-13 14:42:19 | 2023-04-13 14:42:39 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 8 | 2 | I got the following error whenever I try to downlond “CIMLR” packages. ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [CIMLR.so] Error 1 ERROR: compilation failed for package ‘CIMLR’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/CIMLR’ Warning message: In i.p(...) : installation of package ‘/var/folders/t4/cdb0fwxs7z117qqykst9gsnm0000gn/T//RtmpDO43VK/file1554be49d93/CIMLR_1.0.0.tar.gz’ had non-zero exit status | Anonymous Attendee | nan | In the chat I included some trouble-shootinf for MOVICS and CLIMR in Mac. I’ll paste here again. | 2023-04-13 14:42:19 | 2023-04-13 14:43:11 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 9 | 2 | I got the following error whenever I try to downlond “CIMLR” packages. ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.6.0/12.0.1' ld: library not found for -lgfortran clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [CIMLR.so] Error 1 ERROR: compilation failed for package ‘CIMLR’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/CIMLR’ Warning message: In i.p(...) : installation of package ‘/var/folders/t4/cdb0fwxs7z117qqykst9gsnm0000gn/T//RtmpDO43VK/file1554be49d93/CIMLR_1.0.0.tar.gz’ had non-zero exit status | Anonymous Attendee | nan | 0) macOS 13 Ventura 1) Latest R installed 2) R CMD INSTALL /Users/katerinakechris/Desktop/heatmap.plus_1.3.tar.gz 3) Install Xcode (this takes at least 30 minutes) https://developer.apple.com/download/all/?q=Xcode Xcode 14.3 4) In ~/.R/Makevars FC = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran F77 = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 (If doesn’t exit, can create this way: mkdir -p ~/.R) 4) install.packages("BiocManager") install.packages("devtools") install.packages("Matrix", dependencies = TRUE) 5) https://github.com/danro9685/CIMLR library("devtools") install_github("danro9685/CIMLR", ref = 'R') library("CIMLR") 6) devtools::install_github("xlucpu/MOVICS") | 2023-04-13 14:42:19 | 2023-04-13 14:43:56 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 10 | 3 | Testing, testing... | Jennifer Bryant | '- | Thank you! | 2023-04-13 14:42:30 | 2023-04-13 14:43:14 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 11 | 4 | Are these slides on GitHub? | Anonymous Attendee | nan | Yes, please see Lecture2 folder and the “clustering_presentation.pdf” file | 2023-04-13 15:10:17 | 2023-04-13 15:10:53 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 12 | 4 | Are these slides on GitHub? | Anonymous Attendee | nan | https://github.com/KechrisLab/ASAShortCourse-MultiOmics/tree/main/Lecture%202 | 2023-04-13 15:10:17 | 2023-04-13 15:11:13 | Rick Chang | rick.chang@pitt.edu |
| 13 | 5 | I will take a look at the paper as well, but do you happen to remember off hand why mixOmics was not recommended? | Tim Vigers (he/him) | '- | You are correct, the Zhang et al. 2022 does’t include mixOmics. On page 16, I found a sentence that says that they did not include some methods, including ones that are correlation and covariance based (which is the case for mixOmics). | 2023-04-13 15:24:26 | 2023-04-13 15:30:03 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 14 | 5 | I will take a look at the paper as well, but do you happen to remember off hand why mixOmics was not recommended? | Tim Vigers (he/him) | '- | Here is the reference: https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wics.1553 | 2023-04-13 15:24:26 | 2023-04-13 15:30:39 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 15 | 6 | Running R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) Trying to install MOVICS. I get the following error: ERROR: dependencies ‘CIMLR’, ‘SNFtool’ are not available for package ‘MOVICS’. When I run “sessionInfo”, I get the following “> sessionInfo() Error in x$Priority : $ operator is invalid for atomic vectors In addition: Warning message: In FUN(X[[i]], ...) : DESCRIPTION file of package 'SNFtool' is missing or broken” I have installed SNFtool > install.packages("SNFtool") trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/SNFtool_2.3.1.tgz' Content type 'application/x-gzip' length 310241 bytes (302 KB) ================================================== downloaded 302 KB I have tried quitting RStudio and running again. I receive the same error message. | Monnie McGee | '- | For SNFtool, we recommend to install from source. download link: https://cran.r-project.org/src/contrib/Archive/SNFtool/ choose version 2.3.0 and use the following commend to install install.packages("~/Downloads/SNFtool_2.3.0.tar.gz", repos = NULL, type="source") | 2023-04-13 15:24:53 | 2023-04-13 15:27:16 | Rick Chang | rick.chang@pitt.edu |
| 16 | 6 | Running R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) Trying to install MOVICS. I get the following error: ERROR: dependencies ‘CIMLR’, ‘SNFtool’ are not available for package ‘MOVICS’. When I run “sessionInfo”, I get the following “> sessionInfo() Error in x$Priority : $ operator is invalid for atomic vectors In addition: Warning message: In FUN(X[[i]], ...) : DESCRIPTION file of package 'SNFtool' is missing or broken” I have installed SNFtool > install.packages("SNFtool") trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/SNFtool_2.3.1.tgz' Content type 'application/x-gzip' length 310241 bytes (302 KB) ================================================== downloaded 302 KB I have tried quitting RStudio and running again. I receive the same error message. | Monnie McGee | '- | Let me know if you still get error message after installing SNFtool from soruce! | 2023-04-13 15:24:53 | 2023-04-13 15:29:19 | Rick Chang | rick.chang@pitt.edu |
| 17 | 7 | Any help for installing the heatmap package? Still having trouble with this | Daniel Guzman | '- | For heatmap.plus, we recommend to install from source. download link: https://cran.r-project.org/src/contrib/Archive/heatmap.plus/ choose version 1.3 and use the following commend to install install.packages("~/Downloads/heatmap.plus_1.3.tar.gz”, repos = NULL, type="source") | 2023-04-13 15:29:40 | 2023-04-13 15:31:01 | Rick Chang | rick.chang@pitt.edu |
| 18 | 7 | Any help for installing the heatmap package? Still having trouble with this | Daniel Guzman | '- | and probably you need to change the path of that file! | 2023-04-13 15:29:40 | 2023-04-13 15:32:39 | Rick Chang | rick.chang@pitt.edu |
| 19 | 8 | Thank you! I’m having trouble downloading the PDF but will have to try again on the campus network. Mostly I wanted to make sure there isn’t some huge red flag since we’ve used it in a few analyses! | Tim Vigers (he/him) | '- | I think mixOmics is a great set of tools. No red flags from my experience. | 2023-04-13 15:32:51 | 2023-04-13 15:33:35 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 20 | 9 | It seems that heatmap.plus is not available. > install.packages("./SNFtool_2.3.0.tar.gz", repos = NULL, type="source") ERROR: dependency ‘heatmap.plus’ is not available for package ‘SNFtool’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/SNFtool’ Warning in install.packages : installation of package ‘./SNFtool_2.3.0.tar.gz’ had non-zero exit status | Monnie McGee | '- | Yep! you should install heatmap.plus first by following steps 1) download link: https://cran.r-project.org/src/contrib/Archive/heatmap.plus/ 2) choose version 1.3 and use the following commend to install 3) install.packages(“./heatmap.plus_1.3.tar.gz”, repos = NULL, type="source") | 2023-04-13 15:33:05 | 2023-04-13 15:35:23 | Rick Chang | rick.chang@pitt.edu |
| 21 | 9 | It seems that heatmap.plus is not available. > install.packages("./SNFtool_2.3.0.tar.gz", repos = NULL, type="source") ERROR: dependency ‘heatmap.plus’ is not available for package ‘SNFtool’ * removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/SNFtool’ Warning in install.packages : installation of package ‘./SNFtool_2.3.0.tar.gz’ had non-zero exit status | Monnie McGee | '- | sorry for the inconvenience. This package has lots of dependency issue. Let us know if you still get the error message | 2023-04-13 15:33:05 | 2023-04-13 15:37:14 | Rick Chang | rick.chang@pitt.edu |
| 22 | 10 | Great, thank you! | Tim Vigers (he/him) | '- | nan | 2023-04-13 15:36:18 | nan | nan | nan |
| 23 | 11 | I got heatmap.plus and SNFtool to download and install. heatmap.plus must be installed first (for those of you who are still trying to do this). Now it seems that I have exceeding my GitHub hit rate. > devtools::install_github("xlucpu/MOVICS") Downloading GitHub repo xlucpu/MOVICS@HEAD Error: Failed to install 'unknown package' from GitHub: HTTP error 403. API rate limit exceeded for 129.119.55.31. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.) Rate limit remaining: 0/60 Rate limit reset at: 2023-04-13 20:01:23 UTC | Monnie McGee | '- | one quick solution is to disable checking packages dependencies. Try the following commend! devtools::install_github("xlucpu/MOVICS", dependencies = FALSE) | 2023-04-13 15:37:04 | 2023-04-13 15:43:40 | Rick Chang | rick.chang@pitt.edu |
| 24 | 12 | Any recommendations on alternative distance functions for high-dimensional specifically? The euclidean distance doesn't really work well in high dimensions (data points will be on the "crust/sphere around" the space. Why is then the euclidean distance still used in -omics data? | Sandra González Maldonado | '- | Manhattan distance or fractional norms are alternatives that may behave better than Euclidean in sparse high dimensional space. But I think many of them will still suffer from the curse of dimensionality. Feature selection or dimension reduction is often needed first. | 2023-04-13 15:39:32 | 2023-04-13 15:58:05 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 25 | 13 | *high-dimensional data | Sandra González Maldonado | '- | nan | 2023-04-13 15:40:10 | nan | nan | nan |
| 26 | 14 | how long recordings will be available? | Anna Giczewska | '- | We need to check with the ASA SSGG section. But we’ll try to keep the recording available for the next month and see if we can host them longer. | 2023-04-13 15:40:31 | 2023-04-13 15:42:07 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 27 | 15 | Can we use imputation of missing data for SNF analysis? | Hyunkyu Lee | '- | Yes, the package allows for imputation of missing values. | 2023-04-13 15:43:24 | 2023-04-13 15:53:38 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 28 | 16 | '@Rick Chang - I tried disabling checking dependcies. I still run into the same problem with the hit rate. | Monnie McGee | '- | I came across the GitHub issue too. This is what worked for me: To increase your GitHub API rate limit - Use `usethis::browse_github_pat()` to create a Personal Access Token. - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`. | 2023-04-13 15:45:18 | 2023-04-13 15:47:25 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 29 | 16 | '@Rick Chang - I tried disabling checking dependcies. I still run into the same problem with the hit rate. | Monnie McGee | '- | So when I used the first command - browse_github_pat, it sends me to Github and I got a token and then used this function to set it in R: Sys.setenv(GITHUB_PAT = "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") You would need to replace the “ghp …..” part with the token that you get. | 2023-04-13 15:45:18 | 2023-04-13 15:48:19 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 30 | 17 | Do we need to unzip the heatmap gz file? | Jason Nagati | '- | You don’t have to | 2023-04-13 15:45:20 | 2023-04-13 15:45:58 | Wenjia Wang | wew89@pitt.edu |
| 31 | 18 | Says I had to get a newer version of R for the heatmap package. I updated R to the newest version and it still won’t load | Daniel Guzman | '- | you can manually download the zip file of the heatmap.plus pacakge from https://cran.r-project.org/src/contrib/Archive/heatmap.plus/, then run install.packages(path_to_file, repos = NULL, type="source") in R | 2023-04-13 15:47:57 | 2023-04-13 15:50:19 | Wenjia Wang | wew89@pitt.edu |
| 32 | 19 | The installation finally worked after I changed the quotation marks (") around the filename to apostrophes. | Jason Nagati | '- | nan | 2023-04-13 15:48:17 | nan | nan | nan |
| 33 | 20 | Does the heatmap3 package work instead? I was able to install that | Daniel Guzman | '- | Did you use version 1.3? I had the same problem and used this to install after I downladed the package tar R CMD INSTALL /Users/katerinakechris/Desktop/heatmap.plus_1.3.tar.gz | 2023-04-13 15:49:17 | 2023-04-13 15:50:36 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 34 | 21 | Any advice on similarity measures to use for zero inflated data (to be able to use SNF on something like single cell data which is very sparse?)? | Margaret Janiczek | '- | Yes, zero-inflated can be challenging. I think this is ongoing research. Here is a paper that uses a special kernel distance: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359587/ If I find more approaches, I’ll let you know. | 2023-04-13 15:50:13 | 2023-04-13 15:51:04 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 35 | 22 | In step 4, do I need to create Makevars file by my self using textEdit? why not in src/ ? | Anonymous Attendee | nan | Yes if doesn’t exist you’ll need to create it. It’s supposed to be in the ~/.R directory. If that doesn’t exist you can also create that directory: mkdir -p ~/.R | 2023-04-13 15:52:03 | 2023-04-13 15:54:42 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 36 | 23 | I am having this dependency ‘CIMLR’ is not available for package ‘MOVICS’ do we also download CIMLR from souce? | Manni Zhang | '- | 1) In ~/.R/Makevars FC = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran F77 = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 (If doesn’t exit, can create this way: mkdir -p ~/.R) 2) install.packages("BiocManager") install.packages("devtools") install.packages("Matrix", dependencies = TRUE) 3) https://github.com/danro9685/CIMLR library("devtools") install_github("danro9685/CIMLR", ref = 'R') library("CIMLR") | 2023-04-13 15:52:26 | 2023-04-13 15:54:30 | Rick Chang | rick.chang@pitt.edu |
| 37 | 24 | Does this require downloading homebrew? How do you create ~/.R/Makevars? Should this file be in the root directory on the computer? | Monnie McGee | '- | use terminal and use this commend 1) vi ~/.R/Makevars 2) press i 3) copy and paste the following lines FC = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran F77 = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 4) press :wq | 2023-04-13 15:59:27 | 2023-04-13 16:02:49 | Rick Chang | rick.chang@pitt.edu |
| 38 | 24 | Does this require downloading homebrew? How do you create ~/.R/Makevars? Should this file be in the root directory on the computer? | Monnie McGee | '- | use terminal and use this commend 1) vi ~/.R/Makevars 2) press i 3) copy and paste the following lines FC = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran F77 = /opt/homebrew/Cellar/gcc/12.2.0/bin/gfortran FLIBS = -L/opt/homebrew/Cellar/gcc/12.2.0/lib/gcc/12 4) press esc 5) press :wq | 2023-04-13 15:59:27 | 2023-04-13 16:03:27 | Rick Chang | rick.chang@pitt.edu |
| 39 | 24 | Does this require downloading homebrew? How do you create ~/.R/Makevars? Should this file be in the root directory on the computer? | Monnie McGee | '- | The other solution is to install Xcode (but it may take at least 30 minutes) After you installed Xcode, you would be able to install CLIMR using R installation code. No need to create ~/.R/Makevars https://developer.apple.com/download/all/?q=Xcode | 2023-04-13 15:59:27 | 2023-04-13 16:13:55 | Rick Chang | rick.chang@pitt.edu |
| 40 | 25 | Is it advisable to add negative controls when integrating multiomics data? | Joanne TY Lim | '- | I think it depends on the application. The healthy controls may be so different that they drive the signal and it will be harder to identify the more subtle differences between subtypes/clusters, which is often the goal of subtyping methods. | 2023-04-13 16:00:02 | 2023-04-13 16:03:32 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 41 | 26 | i.e. adding healthy controls in a cohort of BRCA cases | Joanne TY Lim | '- | nan | 2023-04-13 16:01:00 | nan | nan | nan |
| 42 | 27 | Could you tell me if this is true? We have Average silhouette width(ASW) close to 1 if we have fewer samples whose SW < 0. | Hyunkyu Lee | '- | Yes, or there may be no negative SW, but the SW are generally large and close to 1. | 2023-04-13 16:12:17 | 2023-04-13 16:15:47 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 43 | 28 | Got it! Finally. I started trying at 1:45 (CDT) today. Bioconductor documentation indicates that CIMLR has been replaced by SIMLR. I guess this is a question for MOVICS developers: Are there plans for updated MOVICS so that it uses SIMLR instead? | Monnie McGee | '- | Yes I agree that’s a good question for the developers. I also found the CIMLR installation the most problematic part of installing MOVICS. It would be important to address this with them. | 2023-04-13 16:14:32 | 2023-04-13 16:17:08 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 44 | 29 | Thank you for your patience and the step-by-step instructions. I don’t use vi often; therefore, I forget the commands. | Monnie McGee | '- | nan | 2023-04-13 16:15:18 | nan | nan | nan |
| 45 | 30 | What does it mean “regulatory”? | Anonymous Attendee | nan | I was busy typing an answer and did not hear the word ‘regulatory’. Perhaps the context is that in these 3 data sets methylation and miRNA can regulate gene expression. Otherwise, let me know the context and I can help answer again. | 2023-04-13 16:17:11 | 2023-04-13 16:19:23 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 46 | 31 | Any advice on whether there is a type of data to which the dimension reduction technique (e.g., PCA) is not applicable? | Hyunkyu Lee | '- | There are various reasons not to apply dimension reduction. For example, PCA is a linear approach and if the data are non-linear that could be problematic. Also if the variables are not that correlated or not small in dimension there may not be much benefit. Also, dimension reduction limits interpretability if that is important for downstream analyses. If it the dimensionality is very large processing power may be an issue. Classical methods like PCA may also be sensitivte to outliers. Having said that, there are a variety of dimension reduction methods so you should check their assumptions and whether they would be a good fit for your problem. | 2023-04-13 16:20:50 | 2023-04-13 16:26:43 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 47 | 32 | Have done everything in the q&a except download xcode but it is still saying Error: Failed to install 'unknown package' from GitHub: HTTP error 403. API rate limit exceeded for 128.210.106.73. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.) Rate limit remaining: 0/60 Rate limit reset at: 2023-04-13 20:44:21 UTC I also tried to specify dependencies = F, same complaint… | Manni Zhang | '- | There is another way to deal with that issue! To increase your GitHub API rate limit - Use `usethis::browse_github_pat()` to create a Personal Access Token. - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`. So when I used the first command - browse_github_pat, it sends me to Github and I got a token and then used this function to set it in R: Sys.setenv(GITHUB_PAT = "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") You would need to replace the “ghp …..” part with the token that you get. | 2023-04-13 16:24:46 | 2023-04-13 16:28:30 | Rick Chang | rick.chang@pitt.edu |
| 48 | 33 | What is the meaning of Up regulatory vs down regulatory? | Anonymous Attendee | nan | Up regualtory means higher expression in one group than the others. | 2023-04-13 16:29:25 | 2023-04-13 16:31:12 | Wenjia Wang | wew89@pitt.edu |
| 49 | 34 | Excellent talk, thank you. | Suzette Blanchard | '- | nan | 2023-04-13 16:30:36 | nan | nan | nan |
| 50 | 35 | Thank you! I’ll try | Manni Zhang | '- | nan | 2023-04-13 16:31:03 | nan | nan | nan |
| 51 | 36 | thank you | Anna Giczewska | '- | nan | 2023-04-13 16:31:40 | nan | nan | nan |
| 52 | 37 | Thank you for the lecture! One quick question: it seems that the multi-omics data do not include germline genetic data. Could you please comment on that? Or any additional papers to refer to? Thank you! | Anonymous Attendee | nan | Based on Sierra’s answers, there are some functions and specifications that allow for this. Check out MOVICS manual. | 2023-04-13 16:33:36 | 2023-04-13 16:38:59 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 53 | 38 | Hello I couldn't see the answer to your last question because I accidentally closed my Zoom meeting. Could you please copy and paste the contents? | Hyunkyu Lee | '- | There are various reasons not to apply dimension reduction. For example, PCA is a linear approach and if the data are non-linear that could be problematic. Also if the variables are not that correlated or not small in dimension there may not be much benefit. Also, dimension reduction limits interpretability if that is important for downstream analyses. If it the dimensionality is very large processing power may be an issue. Classical methods like PCA may also be sensitivte to outliers. Having said that, there are a variety of dimension reduction methods so you should check their assumptions and whether they would be a good fit for your problem. | 2023-04-13 16:33:59 | 2023-04-13 16:34:14 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 54 | 39 | If for genetic variants, do we have to sort of filtering by MAF? also, do we need to consider the sample size? | Anonymous Attendee | nan | elite.tmp <- getElites(dat = tmp, method = "freq", # must set as 'freq' elite.num = 80, # note: in this scenario elite.num refers to frequency of mutation elite.pct = 0.1) | 2023-04-13 16:35:26 | 2023-04-13 16:37:56 | Sierra Niemiec | sierra.niemiec@cuanschutz.edu |
| 55 | 40 | I entered the first command but not directing me to anywhere | Manni Zhang | '- | It may require a GitHub account, just confirming that you have one? | 2023-04-13 16:35:29 | 2023-04-13 16:36:53 | Nancy Zhang | asa.ssgg2018@gmail.com |
| 56 | 41 | yes! | Manni Zhang | '- | nan | 2023-04-13 16:37:26 | nan | nan | nan |
| 57 | 42 | Got it - thank you! | Anonymous Attendee | nan | nan | 2023-04-13 16:38:26 | nan | nan | nan |