[BioC] edgeR: error in readDGE
whuber at embl.de
Wed Nov 10 10:33:38 CET 2010
It looks like the second column ("COUNT") in your files is not always
numeric. Can you send the output of the following:
for (f in targets$files)
Il Nov/10/10 9:36 AM, 村田 卓也 ha scritto:
> I am a beginner of everything of R and edgeR; just like "copy and paste of the command" of the manual.
> I tried to make DGEList object like descriptions on page 9.
> I could make object, "target", as follows.
> files group description
> 1 GAT.txt MT FT9
> 2 ACA.txt WT FT9
> 3 ACT.txt MT FT10
> 4 ACG.txt WT FT10
> On the next command, I failed.
> d<- readDGE(targets)
> (I deleted "skip = 5, comment.char = "#"" from original command, because on my understanding,
> there were no rows to be skipped, nor comments.)
> error colSums(x$counts) : 'x' must be numeric
> This error message might be inaccurate, because it is localized.
> GAT.txt, and other txt files were made as a tab-delimited, plain-text, as follows, for example.
> SEQUENCE COUNT
> AAACAGCAGAGAGAGAGAGAGAGAGAG 0
> AAACAGCAGGTACAAGATCTACCCGGG 0
> AAACAGCAGTGTTCTGAAGCCAAACTC 0
> I use R for Mac OSX GUI 1.35 and newest edgeR.
> I am very happy, if you have any comments.
> Thank you.
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