[Bioc-sig-seq] edgeR datasets

[Jérôme Laroche]

Hi,

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:

Tag_Sequence    Count
AAAAAAAAAA      17
AAAAAAAAGA      1
AAAAAAACCC      1
AAAAAAAGCA      1
AAAAAAATCA      4

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
> dim(d)
I get "NULL" as a result.


Thank you for your help.

Jerome
Universite Laval, Quebec, Canada