Thanks Gordon I changed the old file reference and made some minor changes in the code. Now, everything is working fine. Best, Marcus On Thu, Jun 23, 2011 at 03:09, Gordon K Smyth <smyth@wehi.edu.au> wrote: > Hi Marcus, > > The file you want is called "genelist.txt". You can use this in place of > "091701RikenUpdatev3.txt". This is a simplified version of the complete > probe annotation file "091701RikenUpdatev3.txt", in which the gene > identifiers are removed, because I didn't have permission to make the > complete data publicly available. The "spottypes.txt" is also slighltly > different from that used in the limma User's Guide. Sorry for the > confusion. > > Best wishes > Gordon > > Date: Mon, 20 Jun 2011 19:50:01 -0400 >> From: Marcus Nunes <marcus.nunes@gmail.com> >> To: Bioconductor <bioconductor@r-project.org> >> Subject: [BioC] Help with the weaver example from limma package >> Content-Type: text/plain >> >> Hello all >> >> I'm trying to figure out how to mimic the example given in Weaver Mutant >> Data: A 2x2 Factorial Experiment with Two-Color Data (page 81 of this >> manual: >> http://bioconductor.org/**packages/2.6/bioc/vignettes/** >> limma/inst/doc/usersguide.pdf<http: bioconductor.org="" packages="" 2.6="" bioc="" vignettes="" limma="" inst="" doc="" usersguide.pdf=""> >> ) >> >> There is a line of code, in page 82, that says >> >> Annotation <- read.delim("**091701RikenUpdatev3.txt", header = TRUE, >>> >> comment.char="", >> + quote="\"", as.is = TRUE, check.names=FALSE >> >> I downloaded the dataset available at >> http://bioinf.wehi.edu.au/**limma/data/weaver.zip<http: bioinf.weh="" i.edu.au="" limma="" data="" weaver.zip="">and I can't find this >> file 091701RikenUpdatev3.txt. I already searched the internet and I >> couldn't >> figure out what I have to do. I'll be very glad if you know how to help >> me. >> >> Thanks >> -- >> Marcus Nunes >> > > ______________________________**______________________________**____ ______ > The information in this email is confidential and inte...{{dropped:16}}