Hi Tim, sorry i am very busy and i had no time to answer you, by the way, that's my code library(gplots) #Load libraries library(exonmap) library(plier) library(limma) library(hugene10stprobeset.db) library(hugene10sttranscriptcluster.db) raw.data<-read.exon(covdesc="covdesc") dat <- ReadAffy(cdfname="hugene10stv1cdf") #alternative using hugene10stv1cdf in order to avoid problems with the probesetidd ####DON'T USE IT!!!raw.data at cdfName<-"exon.pmcdf"# which CDF file defines the array by setting the name of the .cdf #checking consistency of the data summary(exprs(raw.data)) #RMA normalization and generate probeset summaries x.rma<-rma(raw.data) #PLIER normalization and generate probeset summaries x.pli<-justPlier(raw.data, usemm=F, normalize=T, norm.type="pmonly") #calculating fold changes and p-values pc.rma <-pc(x.rma,"group",c("a","b"))## for rma normalization pc.pli <-pc(x.pli,"group",c("a","b"))## for plier normalization #find all probesets with an absolute fold change greater than 2 and unadjusted p-value less than 10e-4 keep.data<-(abs(fc(pc.rma))>2) &tt(pc.rma)<1e-4### only 2 keep.data.rma<-(abs(fc(pc.rma))>2) &tt(pc.rma)<1e-2### >260 Use this!!!!!!!!!!! For rma keep.data.pli<-(abs(fc(pc.pli))>2) &tt(pc.pli)<1e-2### >106 Use this!!!!!!!!!!! for plier #fishes thenames of these probesets out form raw.data objects sigs.rma<-featureNames(x.rma)[keep.data.rma]### Caution!!! must be determined if this command exists in xmapcore or has been overwrited/substituted!!!! sigs.pli<-featureNames(x.pli)[keep.data.pli]### Caution!!! must be determined if this command exists in xmapcore or has been overwrited/substituted!!!! ####ALTERNATIVELY CALCULATING FOLD CHANGE USING LIMMA design<-as.matrix(cbind(DKO=c(1,1,1,1,1,1,0,0,0,0,0,0),WT=c(0,0,0,0,0, 0,1,1,1,1,1,1))) fit.rma<-lmFit(x.rma,design)## For rma fit.plier<-lmFit(x.pli,design)# For plier cont.matrix<-makeContrasts(DKOvsWT=DKO-WT,levels=design) fit2.rma<-contrasts.fit(fit.rma,cont.matrix) fit2.pli<-contrasts.fit(fit.plier,cont.matrix) fit3.rma<-eBayes(fit2.rma) fit3.pli<-eBayes(fit2.pli) result.fold.limma.rma<-decideTests(fit3.rma, lfc=2) result.fold.limma.pli<-decideTests(fit3.pli, lfc=2) keep.limma.rma<-result.fold.limma.rma@".Data" !=0 keep.limma.pli<-result.fold.limma.pli@".Data" !=0 limma.sigs.rma<-rownames(result.fold.limma.rma@".Data")[keep.limma.rma ] limma.sigs.pli<-rownames(result.fold.limma.pli@".Data")[keep.limma.pli ] ##### ##### Exporting the data in order to be used with xmapcore script v<-as.data.frame(limma.sigs.pli)#### coercing the vector into a data frame sink("significant_probesets_limma_plier.csv") write.table(v, quote = FALSE, sep = ",")# exporting the data as csv file sink() detach(exonmap) #####MAPPING TO ANNOTATION ##### Which transcripts are differentially expressed??? library(xmapcore) library(exon.pmcdf) Sys.setenv(R_XMAP_CONF_DIR="~/.exonmap")#configuring XMAP_DIR xmap.connect()##connecting to the database probeset.to.trancript(sigs) #### HERE ARE THE NULL RESULTS!!!!!!!!!!! I guess that the problem is that i'm using the results from a Human Gene 1.0 ST array and i don't know if exonmap is able to handle this data in order to find exons. I checked the probesets that i obtained using featureNames in HuGene-1_0-st-v1.na30.1.hg19.probeset files and i found that the code obtained is transcript_cluster_id and no from probesets. Is xmapcore able to handle those transcripts ids or may i have to use another package as xps or affygui in order to translate this ids to probesets or gene ids previous to the use of xmapcore? Thanks in advance ________________________________________ De: Tim Yates [tyates at picr.man.ac.uk] Enviat el: diumenge, 1 / maig / 2011 12:22 Per a: Gomez Moruno, Antonio; bioconductor at r-project.org Tema: Re: [BioC] problems with Affymetrix probes id using exonmap and xmapcore Hi again Sorry for the late responses, it's a big public holiday here in the UK... Can you give an example of the code which is returning NULL? Cheers, Tim On 28/04/2011 16:05, "Gomez Moruno, Antonio" <agomezm at="" idibell.cat=""> wrote: > Hi Tim, > > the problem is that i need to process the data previously with exonmap and > then try to annotate this data with xmapcore. Could it be possible? From your > reply i assume that i can normalize the data and work with probesets using > only xmapcore?? But, i read the doc concerning xmapcore and i didn't find > nothing about it. > > I tried to use another Affymetrix related package, oligo, and i obtained this > info about my data > > ExpressionSet (storageMode: lockedEnvironment) > assayData: 257430 features, 12 samples > element names: exprs > protocolData > rowNames: IG100120JMI035-3gst_01.CEL IG100120JMI036-3gst_01.CEL ... > IG100120JMI046-3gst_01.CEL (12 total) > varLabels: exprs dates > varMetadata: labelDescription channel > phenoData > rowNames: IG100120JMI035-3gst_01.CEL IG100120JMI036-3gst_01.CEL ... > IG100120JMI046-3gst_01.CEL (12 total) > varLabels: index > varMetadata: labelDescription channel > featureData > featureNames: 7892501 7892502 ... 8180418 (257430 total) > fvarLabels: probesetid seqname ... probesettype (39 total) > fvarMetadata: labelDescription > experimentData: use 'experimentData(object)' > Annotation: pd.hugene.1.0.st.v1 > > So, the numbers that i got here are the same that i got in exonmpa, how can i > handle this on xmapcore?? > > Thanks > > ________________________________________ > De: Tim Yates [TYates at picr.man.ac.uk] > Enviat el: dijous, 28 / abril / 2011 15:20 > Per a: Gomez Moruno, Antonio > Tema: Re: [BioC] problems with Affymetrix probes id using exonmap and xmapcore > > Hiya, > > You seem to have both the deprecated exonmap package, and the xmapcore package > loaded at the same time. > > This will cause misbehavior at best, and crashes at worst. > > Can you try with just xmapcore loaded, and if that still doesn't work, can you > post a failing example of your code? > > Cheers, > > Tim > > > > ----- Reply message ----- > From: "Gomez Moruno, Antonio" <agomezm at="" idibell.cat=""> > Date: Thu, Apr 28, 2011 08:58 > Subject: [BioC] problems with Affymetrix probes id using exonmap and xmapcore > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > > I got several .CEL files to do RMA using exonmap library, when i got my list > significant differentially expressed probesets and i try to use xmapcore to > map to annotation using "exonic", all i got is a NULL vector. I used xmapcore > examples and all worked perfectly, but my list of Probesets have no > correspondance in xmapcore. Anyone has any idea? > > This is my session info > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hugene10stv1cdf_2.8.0 hugene10sttranscriptcluster.db_7.0.1 > [3] hugene10stprobeset.db_7.0.1 org.Hs.eg.db_2.5.0 > [5] RSQLite_0.9-4 AnnotationDbi_1.14.1 > [7] limma_3.8.1 plier_1.22.0 > [9] exon.pmcdf_1.1 xmapcore_1.6.0 > [11] IRanges_1.10.0 RMySQL_0.7-5 > [13] DBI_0.2-5 RColorBrewer_1.0-2 > [15] genefilter_1.34.0 affy_1.30.0 > [17] Biobase_2.12.1 exonmap_2.0.03 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 annotate_1.30.0 digest_0.4.2 > [4] preprocessCore_1.14.0 splines_2.13.0 > [7] survival_2.36-8 tools_2.13.0 xtable_1.5-6 > > this is my raw data > > AffyBatch object > size of arrays=1050x1050 features (21 kb) > cdf=exon.pmcdf (1411189 affyids) > number of samples=12 > number of genes=1411189 > annotation=hugene10stv1 > notes= > > > > > Thanks in advance > _______________________________________________ > 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 > -------------------------------------------------------- > This email is confidential and intended solely for the...{{dropped:29}}