Entering edit mode
I am following the GAGE pathway analysis workflow from the 'gene_exp.diff' file produced by Cuffdiff v1.3.0 (part 7.5 here) and get the following error:
# Cuffdiff fork cuff.res=read.delim(file="/home/user/gene_exp.diff", sep="\t") #notice the column name special character changes. The column used to be #cuff.res$log2.fold_change. for older versions of Cufflinks. cuff.fc=cuff.res$log2.FPKMy.FPKMx. gnames=cuff.res$gene sel=gnames!="-" gnames=as.character(gnames[sel]) cuff.fc=cuff.fc[sel] names(cuff.fc)=gnames Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
What does the error mean? I checked my 'gene' column on the 'gene_ex.diff' but I don't have any blank field (or the problem is not related to this column at all?)
Just figured it out. My version of Cuffdiff still used 'log2.fold_change' and not 'log2.FPKMy.FPKMx.'
Works now, except I have a segfault problem with Pathview now. Please see Pathview: *** caught segfault *** cause 'memory not mapped'