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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
