[Bioc-sig-seq] edgeR datasets
jerome.laroche at ibis.ulaval.ca
Thu Aug 11 20:17:06 CEST 2011
I try to replicate the analysis "Case study of SAGE data" presented on page 9 of edgeR document. I wonder if the mentioned datasets of Zhang et al. 1997 are available somewhere? The datasets are: GSM728.txt, GSM729.txt, GSM755.txt, GSM756.txt and particularly Targets.txt.
I looked at the page http://sites.google.com/site/davismcc/useful-documents, but they do not seem to be there.
I tried to work with the files that accompany the package (NC1.txt, NC2.txt, and Tu98.txt Tu102.txt) but I get an error message when I run the command:
> d <- calcNormFactors (d)
(Error in calcNormFactors (d) 'data matrix' Need to Be a matrix).
All the files are in the form:
and the Targets.txt file is:
files group description
NC1.txt NC Normal colon
NC2.txt NC Normal colon
Tu98.txt Tu Primary colonrectal tumour
Tu102.txt Tu Primary colonrectal tumour
In fact, after running the commands:
> targets <-read.delim (file = "Targets.txt" stringsAsFactors = FALSE)
> d <- readDGE (targets, skip = 5, comment.char ="!")
I do not get a column showing the normalization factors (1 for all files) as shown in the document.
Also, when I run the command
I get "NULL" as a result.
Thank you for your help.
Universite Laval, Quebec, Canada
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