problems with Affymetrix probes id using exonmap and xmapcore
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Tim Yates ▴ 250
@tim-yates-4040
Last seen 8.4 years ago
Sorry, my phone decided to send this response off list... --- 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 On 28/04/2011 08:54, "Gomez Moruno, Antonio" <agomezm at="" idibell.cat=""> wrote: > 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 u...{{dropped:12}}
Annotation cdf exonmap xmapcore Annotation cdf exonmap xmapcore • 780 views
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Tim Yates ▴ 250
@tim-yates-4040
Last seen 8.4 years ago
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 use of the person(s) > ('the intended recipient') to whom it was addressed. Any views or opinions > presented are solely those of the author and do not necessarily represent > those of the Paterson Institute for Cancer Research or the University of > Manchester. It may contain information that is privileged & confidential > within the meaning of applicable law. Accordingly any dissemination, > distribution, copying, or other use of this message, or any of its contents, > by any person other than the intended recipient may constitute a breach of > civil or criminal law and is strictly prohibited. If you are NOT the intended > recipient please contact the sender and dispose of this e-mail as soon as > possible. -------------------------------------------------------- This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the University of Manchester. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible.
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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}}
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