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ComBat_seq cannot be found #5
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Did you load the library? After installing the devel version, make sure you load/attach it:
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I think I actually did. I could use the old version of |
Hi, I am also not able to find ComBat_seq upon package installation. can you please make it available through Bioconductor SVA version also. Thanks |
Hi, I also cannot find the ComBat_seq function via "sva" package. Is this function no longer available? |
@Zepeng-Mu @madhulika-EBI @PrincescaDorsaint ComBat-Seq is already available in the development version of Bioconductor, which I believe requires R > 4.0. https://www.bioconductor.org/packages/devel/bioc/html/sva.html If you do not want to update your R version to use devel Bioconductor, you can 1) wait until the next Bioconductor release, 2) clone the GitHub repo and use source to load ComBat_seq, as @Zepeng-Mu suggests, or 3) use the sva package on my github devtools::install_github("zhangyuqing/sva-devel"). With 3), make sure to remove the previous sva installed on your laptop: remove.packages("sva") before installing. After installation, check packageVersion("sva") to make sure it is version 3.35.2. This works on my laptop, and I'm able to find ComBat_seq function. If you still can't find it, there are suggested steps you can try to fix the issue: https://stackoverflow.com/questions/7027288/error-could-not-find-function-in-r |
None of the options suggested works for me. Am I the only one having this issue? |
I installed sva 3.38.0 from bioconductor and it has the |
Apparently, I had an issue with the installation. Now working! Thanks! |
How to use source to load it |
@zhangyuqing
Update: I did it the source way |
@daixiaozhuan You can do it as below: |
Hi, I installed the package from GitHub repo sva-devel. I can see the document page of
ComBat_seq
but when I try to run the function, I got "could not find function "ComBat_seq".The text was updated successfully, but these errors were encountered: