[BioC] ERROR: Length of \'group\' must equal number of columns in \'data\'

[Mark Robinson]

Hi Cawendish (?),

You are using a *very* old version of edgeR and of R.  Nearly 3 years in R/Bioconductor time is quite like an eternity.  R 2.15 was just released, so I would consider installing that one.  Then, install edgeR with:

source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")

And, then try your commands again.

And if you aren't already, be sure to read an updated version of the User's guide:
http://www.bioconductor.org/packages/release/bioc/html/edgeR.html

Best,
Mark


On 05.04.2012, at 14:48, aliaselin [guest] wrote:

> 
> I'm trying to use edgeR to analyse RNA-seq data following the guidance of "edgeR: differential expression analysis of digital gene expression data".
> I have done exactly as the manual told and when tapping the command "d <-
> DGEList(counts=d, group=group)", then an error comes as "错误于DGEList(counts = d, group = group) : 
>  Length of 'group' must equal number of columns in 'data'
> " 
> 
> However, length(group) shows that the length of the group is 7, and dim(d) = 37435     7.
> So I think they two are equal, so why I got this error?
> Many thanks!
> 
> -- output of sessionInfo(): 
> 
> R version 2.9.1 (2009-06-26) 
> x86_64-redhat-linux-gnu 
> 
> locale:
> LC_CTYPE=zh_CN.UTF-8;LC_NUMERIC=C;LC_TIME=zh_CN.UTF-8;LC_COLLATE=zh_CN.UTF-8;LC_MONETARY=C;LC_MESSAGES=zh_CN.UTF-8;LC_PAPER=zh_CN.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=zh_CN.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] edgeR_1.2.4   Biobase_2.4.1
> 
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor



----------
Prof. Dr. Mark Robinson
Bioinformatics
Institute of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
8057 Zurich
Switzerland

v: +41 44 635 4848
f: +41 44 635 6898
e: mark.robinson at imls.uzh.ch
o: Y11-J-16
w: http://tiny.cc/mrobin