User: leonmcswain

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leonmcswain10
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Posts by leonmcswain

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Comment: C: Tale as old as time: lmFit dimension issues
... I am a Cancer Biologist by training so I still have a bit of work to do regarding R basics (re not introducing these issues to begin with) ...
written 15 days ago by leonmcswain10
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Comment: C: Tale as old as time: lmFit dimension issues
... dariober was correct about this. ...
written 15 days ago by leonmcswain10
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Comment: C: Tale as old as time: lmFit dimension issues
... I already have an answer to the post but I would like to know more about this. When I post should I just copy and paste the output from dput? For this matrix its a bit chaotic since there are 763 columns. The output gets cut off in the console because its so long. ...
written 15 days ago by leonmcswain10
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Comment: C: Tale as old as time: lmFit dimension issues
... This worked perfectly! Thank you! You were also correct about the vector it doesn't matter if I state that because the vector goes into design matrix not directly into lmFit. -Leon ...
written 15 days ago by leonmcswain10
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Tale as old as time: lmFit dimension issues
... I have seen some other posts on here but after going through them Im not finding a solution. I am using limma to do DE analysis on 763 patient microarrays, 4 groups total. My expression object is a matrix with rownames as genes and colnames as patient ID. When I try to run the code I get the error ...
R written 16 days ago by leonmcswain10 • updated 15 days ago by dariober11k
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Comment: C: Issues with STAR aligner install
... How do I remove the compiled files to "clean"? When I delete the STAR file and reinstall followed by compiling it shows compiled files like the files were never deleted. ...
written 3 months ago by leonmcswain10
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Comment: C: Issues with STAR aligner install
... This came at the end when compiling was finished and I am not sure if its significant or not. Parameters_openReadsFiles.cpp: In member function 'void Parameters::openReadsFiles()': Parameters_openReadsFiles.cpp:25:20: warning: variable 'imate' might be clobbered by 'longjmp' or 'vfork' [-Wclobbere ...
written 3 months ago by leonmcswain10
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Comment: C: Issues with STAR aligner install
... I found a solution. I uninstalled all gcc compilers other than gcc@8 and then changed the make directory to match the gcc@8 and it worked. ...
written 3 months ago by leonmcswain10
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Comment: C: Issues with STAR aligner install
... When I type which g++ I get usr/bin/g++ if I type which g++-8 I don't get anything. I used git clone to clone STAR through the terminal onto a file on my desktop (running this on mac). When I check the path (I realize the way I've done it below is not efficient) I find the gcc version is 10.1.0 and ...
written 3 months ago by leonmcswain10
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Issues with STAR aligner install
... I am running into some issues installing STAR aligner. I attempted to follow others solutions. Ive re-installed gcc thinking this was the issue while compiling but I am still getting an error: leonfoymcswain@Leons-MBP ~ % cd ~/Desktop/Bio_Packages/STAR/source leonfoymcswain@Leons-MBP source ...
alignment star rna-seq written 3 months ago by leonmcswain10 • updated 3 months ago by h.mon31k

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