Unable to read Affy Mouse Exon 1.0 ST array CEL file
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@dai-hongying-4801
Last seen 7.1 years ago
Hi, I try to import CEL files generated from Affy Mouse Exon 1.0 ST array. I have tried both Affy and Oligo packages and my computer has 2.75GB RAM. * Please let me know the following issue is package issue or computer RAM issue. * Can any one share code to read Affy Mouse Exon 1.0 ST array CEL files? Below is what I have tried so far. I have highlighted the error code and error message in red. All the other scripts ran well. I find pd.moex.1.0.st.v1 annotation package which provides Platform Design Info for Affymetrix MoEx-1_0-st-v1. First, I tried to import 12 CEL files using affy package: >library(affy) >library(pd.moex.1.0.st.v1) > a1<-ReadAffy() Error: cannot allocate vector of size 600.0 Mb In addition: Warning messages: 1: In read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : Reached total allocation of 1535Mb: see help(memory.size) Secondly, I tried to import 1 CEL file using affy package each time and then combine these CEL files. >fns <- list.celfiles(full.names=TRUE) >temp1<-ReadAffy(filenames=fns[1]) #read 1 CEL, it works >temp2<-ReadAffy(filenames=fns[2]) #read another one CEL, it works > data<-merge.AffyBatch(temp1, temp2) Error: cannot allocate vector of size 100.0 Mb In addition: Warning messages: 1: In do.call(assayDataNew, c(list(exprs = exprs), dots)) : Reached total allocation of 1535Mb: see help(memory.size) Thirdly, I tried to perform gcrma analysis to 1 CEL. >lirary(gcrma) > eset1 <- gcrma(temp1) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain MoEx-1_0-st-v1 Library - package moex10stv1cdf not installed Bioconductor - moex10stv1cdf not availableI then redo the code Fourthly, I tried to add in annotation file when reading 1 CEL file. > a1<-ReadAffy(filenames=fns[1],cdfname="pd.moex.1.0.st.v") Error: cannot allocate vector of size 50.0 Mb In addition: Warning messages: 1: In unlist(vlist, recursive = FALSE, use.names = FALSE) : Reached total allocation of 1535Mb: see help(memory.size) After failure with appy package, I switched to oligo package to read 12 CEL files again. >library(oligo) >exonCELs <- list.celfiles(full.names = TRUE) >affyExonFS <- read.celfiles(exonCELs) Platform design info loaded. Error: cannot allocate vector of size 600.0 Mb In addition: Warning messages: 1: In smartReadCEL(filenames, sampleNames, headdetails = headdetails) : Reached total allocation of 1535Mb: see help(memory.size) Daisy ________________________________ Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer@cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 2 days ago
United States
install.packages("ff") library(ff) then run library(oligo) exonCELs <- list.celfiles(full.names = TRUE) and so on it might help you get through this with smaller consumption On Wed, Aug 10, 2011 at 2:37 PM, Dai, Hongying, <hdai@cmh.edu> wrote: > Hi, > > I try to import CEL files generated from Affy Mouse Exon 1.0 ST array. I > have tried both Affy and Oligo packages and my computer has 2.75GB RAM. > > * Please let me know the following issue is package issue or > computer RAM issue. > > * Can any one share code to read Affy Mouse Exon 1.0 ST array CEL > files? > > Below is what I have tried so far. I have highlighted the error code and > error message in red. All the other scripts ran well. > > I find pd.moex.1.0.st.v1 annotation package which provides Platform Design > Info for Affymetrix MoEx-1_0-st-v1. > > First, I tried to import 12 CEL files using affy package: > > >library(affy) > > >library(pd.moex.1.0.st.v1) > > > a1<-ReadAffy() > > Error: cannot allocate vector of size 600.0 Mb > > In addition: Warning messages: > > 1: In read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > > Reached total allocation of 1535Mb: see help(memory.size) > > Secondly, I tried to import 1 CEL file using affy package each time and > then combine these CEL files. > > >fns <- list.celfiles(full.names=TRUE) > > >temp1<-ReadAffy(filenames=fns[1]) #read 1 CEL, it works > > >temp2<-ReadAffy(filenames=fns[2]) #read another one CEL, it works > > > data<-merge.AffyBatch(temp1, temp2) > > Error: cannot allocate vector of size 100.0 Mb > > In addition: Warning messages: > > 1: In do.call(assayDataNew, c(list(exprs = exprs), dots)) : > > Reached total allocation of 1535Mb: see help(memory.size) > > Thirdly, I tried to perform gcrma analysis to 1 CEL. > > >lirary(gcrma) > > > eset1 <- gcrma(temp1) > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain MoEx-1_0-st-v1 > > Library - package moex10stv1cdf not installed > > Bioconductor - moex10stv1cdf not availableI then redo the code > > Fourthly, I tried to add in annotation file when reading 1 CEL file. > > > a1<-ReadAffy(filenames=fns[1],cdfname="pd.moex.1.0.st.v") > > Error: cannot allocate vector of size 50.0 Mb > > In addition: Warning messages: > > 1: In unlist(vlist, recursive = FALSE, use.names = FALSE) : > > Reached total allocation of 1535Mb: see help(memory.size) > > After failure with appy package, I switched to oligo package to read 12 CEL > files again. > > >library(oligo) > > >exonCELs <- list.celfiles(full.names = TRUE) > > >affyExonFS <- read.celfiles(exonCELs) > > Platform design info loaded. > > Error: cannot allocate vector of size 600.0 Mb > > In addition: Warning messages: > > 1: In smartReadCEL(filenames, sampleNames, headdetails = headdetails) : > > Reached total allocation of 1535Mb: see help(memory.size) > > > > > Daisy > > > > > > > > > > > > > > > > > > > ________________________________ > Electronic mail from Children's Mercy Hospitals and Clinics. This > communication is intended only for the use of the addressee. It may contain > information that is privileged or confidential under applicable law. If you > are not the intended recipient or the agent of the recipient, you are hereby > notified that any dissemination, copy or disclosure of this communication is > strictly prohibited. If you have received this communication in error, > please immediately forward the message to Children's Mercy Hospital's > Information Security Officer via return electronic mail at > informationsecurityofficer@cmh.edu and expunge this communication without > making any copies. Thank you for your cooperation. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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cstrato ★ 3.9k
@cstrato-908
Last seen 3.0 years ago
Austria
Dear Daisy, You could try package "xps" which does not have memory limitations. Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 8/10/11 8:37 PM, Dai, Hongying, wrote: > Hi, > > I try to import CEL files generated from Affy Mouse Exon 1.0 ST array. I have tried both Affy and Oligo packages and my computer has 2.75GB RAM. > > * Please let me know the following issue is package issue or computer RAM issue. > > * Can any one share code to read Affy Mouse Exon 1.0 ST array CEL files? > > Below is what I have tried so far. I have highlighted the error code and error message in red. All the other scripts ran well. > > I find pd.moex.1.0.st.v1 annotation package which provides Platform Design Info for Affymetrix MoEx-1_0-st-v1. > > First, I tried to import 12 CEL files using affy package: > >> library(affy) > >> library(pd.moex.1.0.st.v1) > >> a1<-ReadAffy() > > Error: cannot allocate vector of size 600.0 Mb > > In addition: Warning messages: > > 1: In read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > > Reached total allocation of 1535Mb: see help(memory.size) > > Secondly, I tried to import 1 CEL file using affy package each time and then combine these CEL files. > >> fns<- list.celfiles(full.names=TRUE) > >> temp1<-ReadAffy(filenames=fns[1]) #read 1 CEL, it works > >> temp2<-ReadAffy(filenames=fns[2]) #read another one CEL, it works > >> data<-merge.AffyBatch(temp1, temp2) > > Error: cannot allocate vector of size 100.0 Mb > > In addition: Warning messages: > > 1: In do.call(assayDataNew, c(list(exprs = exprs), dots)) : > > Reached total allocation of 1535Mb: see help(memory.size) > > Thirdly, I tried to perform gcrma analysis to 1 CEL. > >> lirary(gcrma) > >> eset1<- gcrma(temp1) > > Error in getCdfInfo(object) : > > Could not obtain CDF environment, problems encountered: > > Specified environment does not contain MoEx-1_0-st-v1 > > Library - package moex10stv1cdf not installed > > Bioconductor - moex10stv1cdf not availableI then redo the code > > Fourthly, I tried to add in annotation file when reading 1 CEL file. > >> a1<-ReadAffy(filenames=fns[1],cdfname="pd.moex.1.0.st.v") > > Error: cannot allocate vector of size 50.0 Mb > > In addition: Warning messages: > > 1: In unlist(vlist, recursive = FALSE, use.names = FALSE) : > > Reached total allocation of 1535Mb: see help(memory.size) > > After failure with appy package, I switched to oligo package to read 12 CEL files again. > >> library(oligo) > >> exonCELs<- list.celfiles(full.names = TRUE) > >> affyExonFS<- read.celfiles(exonCELs) > > Platform design info loaded. > > Error: cannot allocate vector of size 600.0 Mb > > In addition: Warning messages: > > 1: In smartReadCEL(filenames, sampleNames, headdetails = headdetails) : > > Reached total allocation of 1535Mb: see help(memory.size) > > > > > Daisy > > > > > > > > > > > > > > > > > > > ________________________________ > Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. > > [[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 >