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.laro...@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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing [https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing] ----------------------------------------------------------- Il Contenuto del presente messaggio potrebbe contenere informazioni confidenziali a favore dei soli destinatari del messaggio stesso. Qualora riceviate per errore questo messaggio siete pregati di cancellarlo dalla memoria del computer e di contattare i numeri sopra indicati. Ogni utilizzo o ritrasmissione dei contenuti del messaggio da parte di soggetti diversi dai destinatari è da considerarsi vietato ed abusivo. The information transmitted is intended only for the per...{{dropped:10}}
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