ialbert
commented
2 years ago I am running this exact same code today (a few minutes ago actually, as I am preparing for a lecture) and I am using BigSur 11.6 and did work,
alas but I do know that sometimes things can get out of sync if other packages get installed.
I also tried the following as an alternative and perhaps you can try it yourself:
conda create -n stats -y
conda activate stats
mamba install bioconductor-edger bioconductor-deseq2 r-gplots -y
cat counts.txt | deseq2.r 3x3 > deseq2-results.csvsee if that helps, a brand new environment with minimal dependencies, not even python
EMDLvdHeijden
I have been following the step-by-step tutorial for RNA-seq, which thus far has been great. Thanks so much for creating this content! It's very useful.
I've now reached the chapter where the differential expression analysis is done using either DESeq2 or EdgeR using these commands:
cat counts.txt | deseq2.r 3x3 > deseq2-results.csvor
cat counts.txt | edger.r 3x3 > edger-results.csvHowever, I am unable to do either. I get the following errors:
Error: package or namespace load failed for 'S4Vectors' in library.dynam(lib, package, package.lib): shared object 'S4Vectors.dylib' not found Error: package 'S4Vectors' could not be loaded Execution halted (stats)
running deseq2.r
or
Error: package or namespace load failed for 'limma': .onLoad failed in loadNamespace() for 'limma', details: call: library.dynam("limma", pkgname, libname) error: shared object 'limma.dylib' not found Error: package 'limma' could not be loaded Execution halted (stats)
running edger.r
I checked various things.
First: am I in the right environment? Yes - I'm in stats. Second: are limma and S4vectors installed? Yes - running
conda listin the stats environment tells me they are. Third: maybe there is an issue with the basic set-up? Running doctor.py in the bioinfo environment tells me all is OK. Fourth: total re-install of the entire set-up:rm -rf ~/miniconda3followed bycurl http://data.biostarhandbook.com/install.sh | bash. Randoctor.pyagain in the bioinfo environment (all OK) and a re-install of the stats environment usingconda create --name stats python=3.8 -y,conda activate statsandURL=http://data.biostarhandbook.com/books/rnaseq/code/rnaseq-conda.txtcurl $URL | xargs mamba install -y. I checked whether the installation was correct by just runningdeseq2.ras suggested and that gives the expected error. Everything looks good up to this point. But I still I get the same issue. So I'm stuck.I'm not really sure what else I can do? Am I missing something or doing something wrong?
I am on MacOSX running Big Sur 11.6.
Thanks in advance.