Maggie, seriously, **please keep this on the mailing list**. For the moment, keep your code simple: library(oligo) raw <- read.xysfiles(xys.files) eset <- rma(raw) Then inspect the featureNames(eset). best, b 2011/7/20 ?? <gtzxchj at="" hotmail.com="">: > Dear Professor, > Thank you for your reply! > In my opinion, the genomic annotation you meant is the annotation package I > made beforehand("pd.090319.zea.kr.exptil"), yeah? I have written part of my > script and the error I run into below so that you can exam it and help me > with it! > >>library("pd.090319.zea.kr.exptil") > >> maqc <- read.xysfiles(xys.files) > >> pd <- list.files(dir ,pattern = "phenoData",full.names = TRUE) > >> phenoData(maqc) <- read.AnnotatedDataFrame(pd) > >> class(maqc) > >> eset <- rma(maqc) > > Background correcting > > Normalizing > > Calculating Expression > > error in : validObject(out) : > > invalid class "ExpressionSet" object: 1: sampleNames differ between > assayData and phenoData > > invalid class "ExpressionSet" object: 2: sampleNames differ between > phenoData and protocolData > > Thank you very much!! > > Best Regards > > Maggie > >> From: beniltoncarvalho at gmail.com >> Date: Wed, 20 Jul 2011 12:11:34 +0100 >> Subject: Re: [BioC] Problem about extracting interest data from NimbleGen >> oligo array >> To: gtzxchj at hotmail.com >> >> Maggie, >> >> You need to provide more details and exactly what you have done so >> far. From what you describe, after preprocessing your data, you need >> to load the you refer to and merge with the >> preprocessed results. >> >> Please, keep this conversation on the mailing list, so others can benefit. >> >> b >> >> On 20 July 2011 02:03, ?? <gtzxchj at="" hotmail.com=""> wrote: >> > >> > Dear Professor,I have searched many relevant questions about my topic in >> > mailing list, but why can't I read them from my computer. It always warns: >> > unable to visit, so I have to submit my problem via email. I learned from >> > databases that the ID of Nimblegen probes are members of gene ID. I use >> > commands such as agrep("GRMZM2G425430_T01",featureNames(eset)) to extract >> > the location info of the data I need, but it always returned >> > :integer(0).Could you tell me why and How can I find the data of interest >> > correctly from NimbleGen expression array?Thanks a lot!!Yours >> > sincerelyMaggie >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >> >> -- >> Successful people ask better questions, and as a result, they get >> better answers. (Tony Robbins) > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)