GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
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user31888 ▴ 30
@user31888-9209
Last seen 2.8 years ago
United States

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?) 

GAGE Cuffdiff gene names • 906 views
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 3 months ago
United States
Can you do the following lines then post the outputs: str(cuff.fc) str(cuff.res) str(gnames)
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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'

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