My simplest explanation: did you check if the carriage return of the files  
is UNIX
while you are using R on windows ? you can convert these with the Context 
text editor.
It is a subtle - and common - problem when downloading files from the web.

HTH,

Alessandro
-----------------------------------------------------
Alessandro Guffanti - Bioinformatics, Genomnia srl
Via Nerviano, 31 - 20020 Lainate, Milano, Italy
Ph: +39-0293305.700 Fax: +39-0293305.777
http://www.genomnia.com
"If you can dream it, you can do it" (Walt Disney)

-----Original Message-----
 From: Jérôme Laroche <jerome.laroche@ibis.ulaval.ca>
 To: "bioc-sig-sequencing@r-project.org" <bioc-sig-sequencing@r-project.org>
 Date: Thu, 11 Aug 2011 14:17:06 -0400
 Subject: [Bioc-sig-seq] edgeR datasets


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 
[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

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