Can't normalize 300+ HuGene arrays in xps
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Mike Walter ▴ 230
@mike-walter-4000
Last seen 9.6 years ago
Germany
Hi all, I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. library(xps) memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. exonlevel=rep((8192+1024),3) scheme="Scheme_HuGene10stv1r4_na30_hg19.root" gene.scheme <- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, exonlevel=exonlevel, verbose = FALSE) Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", filedir = getwd(), tmpdir = "", update = FALSE, select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) OR data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", method="quantile", select="pmonly", option="transcript:together:none", logbase="0", params=c(0.0), exonlevel=exonlevel) in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? Thank you very much. Best, Mike > sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] xps_1.6.4 loaded via a namespace (and not attached): [1] tools_2.10.1 -- Dr. Michael Walter MFT Services University of T?bingen Calwerstr. 7 72076 T?bingen Tel.: +49 7071 29 83210 Fax. + 49 7071 29 5228 web: www.mft-services.de Confidentiality Note:\ This message is intended only for...{{dropped:9}}
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@susan-r-atlas-2659
Last seen 10.2 years ago
Hi, Try a 64-bit machine. - Susan ---------------------------------------------------------------------- -- > Hi all, > > I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. > > library(xps) > memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. > exonlevel=rep((8192+1024),3) > scheme="Scheme_HuGene10stv1r4_na30_hg19.root" > gene.scheme <- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) > data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) > data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, > exonlevel=exonlevel, verbose = FALSE) > > > Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: > > data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", > filedir = getwd(), tmpdir = "", update = FALSE, > select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) > > data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), > tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) > > OR > > > data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", > method="quantile", select="pmonly", option="transcript:together:none", > logbase="0", params=c(0.0), exonlevel=exonlevel) > > > in both cases the output is "Fehler in .local(object, ...) : error in function ‘Normalize’". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? > > Thank you very much. > > Best, > Mike > > >> sessionInfo() >> > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.6.4 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > > > > > > -- ------------------------------------------------------------------ Susan R. Atlas Research Associate Professor, Physics and Astronomy Director, Center for Advanced Research Computing Director, University of New Mexico Cancer Center Shared Resource for Bioinformatics and Computational Biology Department of Physics & Astronomy MSC07 4220 p: 505.277.1509 1 University of New Mexico e: susie@sapphire.phys.unm.edu Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials [[alternative HTML version deleted]]
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Dear Susan, Please note that package "xps" was created to handle this amount of data on computers with 1-2GB RAM only, especially on WinXP. However, only the verbose output can tell me what the problem might be. Christian On 8/27/10 7:33 PM, Susan R. Atlas wrote: > Hi, > Try a 64-bit machine. > - Susan > > -------------------------------------------------------------------- ---- > >> Hi all, >> >> I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. >> >> library(xps) >> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. >> exonlevel=rep((8192+1024),3) >> scheme="Scheme_HuGene10stv1r4_na30_hg19.root" >> gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) >> data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) >> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, >> exonlevel=exonlevel, verbose = FALSE) >> >> >> Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: >> >> data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", >> filedir = getwd(), tmpdir = "", update = FALSE, >> select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) >> >> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), >> tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) >> >> OR >> >> >> data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", >> method="quantile", select="pmonly", option="transcript:together:none", >> logbase="0", params=c(0.0), exonlevel=exonlevel) >> >> >> in both cases the output is "Fehler in .local(object, ...) : error in function ???Normalize???". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? >> >> Thank you very much. >> >> Best, >> Mike >> >> >>> sessionInfo() >>> >> R version 2.10.1 (2009-12-14) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >> [5] LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xps_1.6.4 >> >> loaded via a namespace (and not attached): >> [1] tools_2.10.1 >> >> >> >> >> >> > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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cstrato ★ 3.9k
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Last seen 6.2 years ago
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Dear Mike, At the moment I do not see any problem with your code. Since you mention that you have successfully used xps with 180 samples and 144 samples, respectively, I assume that you have used the same code as earlier, is this correct? If not, then could you try to run the code on RTerm with a subset of 6 samples only and show me the verbose output. You can do: > celnames <- c("name1", "name2", etc) #the names of 6 of your cel files > data.xps <- root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/"), celnames =celnames) > data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, exonlevel=exonlevel, verbose = TRUE) If this works, then could you try to repeat your run on RTerm with verbose=TRUE and send me the complete output (at least the part that you are able to copy): > data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = TRUE) Please note that it is important for me to see the complete verbose output, since often only this output could show me where the problem is. Some more questions: Did you run R as RGui or from the console as RTerm? Are you sure that you have enough hard disk space since normalize.quantiles() will use a lot of disk space? 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 8/27/10 3:35 PM, Mike Walter wrote: > Hi all, > > I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. > > library(xps) > memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. > exonlevel=rep((8192+1024),3) > scheme="Scheme_HuGene10stv1r4_na30_hg19.root" > gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) > data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) > data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, > exonlevel=exonlevel, verbose = FALSE) > > > Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: > > data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", > filedir = getwd(), tmpdir = "", update = FALSE, > select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) > > data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), > tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) > > OR > > > data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", > method="quantile", select="pmonly", option="transcript:together:none", > logbase="0", params=c(0.0), exonlevel=exonlevel) > > > in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? > > Thank you very much. > > Best, > Mike > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.6.4 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > > > > >
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cstrato ★ 3.9k
@cstrato-908
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Dear Mike, In case that your problem turns out to be a memory-related problem, you can use rma(...,add.data=FALSE,..), which will prevent filling slot "data" with the expression levels. You can then import all normalized data or parts thereof using "export.expr()" or "root.expr()", as the help files show. Thus you could first run rma and then import the results in a separate step: ## rma > data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, exonlevel=exonlevel, add.data=FALSE, verbose = TRUE) ## import subset of trees: ds <- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", as.dataframe=TRUE) ## use subset of trees > sub.rma <- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", c("name1.mdp", "name2", etc)) > str(sub.rma) Maybe after starting a new R-session, you are able to import all trees with "treenames='*'". Please let me know if this could solve your problem. Best regards Christian On 8/27/10 3:35 PM, Mike Walter wrote: > Hi all, > > I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. > > library(xps) > memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. > exonlevel=rep((8192+1024),3) > scheme="Scheme_HuGene10stv1r4_na30_hg19.root" > gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) > data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) > data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, > exonlevel=exonlevel, verbose = FALSE) > > > Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: > > data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", > filedir = getwd(), tmpdir = "", update = FALSE, > select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) > > data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), > tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) > > OR > > > data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", > method="quantile", select="pmonly", option="transcript:together:none", > logbase="0", params=c(0.0), exonlevel=exonlevel) > > > in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? > > Thank you very much. > > Best, > Mike > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.6.4 > > loaded via a namespace (and not attached): > [1] tools_2.10.1 > > > > >
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Dear Christian, Thanks for your help. To answer your questions first: I normally use RGui and my disk space was ~100Gb. I also tried the add.data=FALSE option, without success. So I did RMA normalization with 6 arrays in RTerm as you proposed. This worked fine. So I just tried to run RMA on all arrays on RTerm. Here, I got thousands of error messages after the "compution common mean" step was finished for all arrays. After approx. 20min of error messages scrolling over my screen windows ended R, so I couldn't copy any output. I made a screenshot, which is attached (although it might not make it into the BioC list). Therefore, I tried the stepwise approach in RTerm. To my great surprise, now everything worked fine. There was no error when I started the quantile normlization with the same code as before (except the verbose=TRUE). The median polish afterwards also worked. The output of RTerm is pasted below. So again, thank you very much for your help. Kind regards, Mike > data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = $ + tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = TRUE) Opening file <x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na30_hg19.roo="" t=""> in <read> mode... Creating new file <f: auswertung="" genepi_combined="" quantile.root="">... Opening file <f: auswertung="" genepi_combined="" bkgd_correct.root=""> in <read> mode... Preprocessing data using method <preprocess>... Normalizing raw data... normalizing data using method <quantile>... setting selector mask for typepm <9216> finished filling <324> arrays. computing common mean... finished filling <324> trees. preprocessing finished. > save.image("F:/Auswertung/GENEPI_combined/GENEPI_all_stepwise.RData") > data.mp = summarize.rma(data.norm, filename = "medianpolish", filedir = getw$ + update = FALSE, option = "transcript", exonlevel = exonlevel, xps.scheme =$ Opening file <x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na30_hg19.roo="" t=""> in <read> mode... Creating new file <f: auswertung="" genepi_combined="" medianpolish.root="">... Opening file <f: auswertung="" genepi_combined="" quantile.root=""> in <read> mode... Preprocessing data using method <preprocess>... Converting raw data to expression levels... summarizing with <medianpolish>... setting selector mask for typepm <9216> setting selector mask for typepm <9216> calculating expression for <28829> of <33664> units...Finished. expression statistics: minimal expression level is <3.11771> maximal expression level is <20015.1> preprocessing finished. Opening file <x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na30_hg19.roo="" t=""> in <read> mode... Opening file <f: auswertung="" genepi_combined="" medianpolish.root=""> in <read> mode... Opening file <f: auswertung="" genepi_combined="" medianpolish.root=""> in <read> mode... Exporting data from tree <*> to file <f: auswertung="" genepi_combined="" medianpolish="" .txt="">... Reading entries from <hugene-1_0-st-v1.ann> ...Finished <28829> of <28829> records exported. -----Urspr?ngliche Nachricht----- Von: cstrato <cstrato at="" aon.at=""> Gesendet: 27.08.2010 21:05:46 An: Mike Walter <michael_walter at="" email.de=""> Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps >Dear Mike, > >In case that your problem turns out to be a memory-related problem, you >can use rma(...,add.data=FALSE,..), which will prevent filling slot >"data" with the expression levels. You can then import all normalized >data or parts thereof using "export.expr()" or "root.expr()", as the >help files show. > >Thus you could first run rma and then import the results in a separate step: > >## rma > > data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", >normalize=T, exonlevel=exonlevel, add.data=FALSE, verbose = TRUE) > >## import subset of trees: >ds <- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), >treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", >as.dataframe=TRUE) > >## use subset of trees > > sub.rma <- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", >c("name1.mdp", "name2", etc)) > > str(sub.rma) > >Maybe after starting a new R-session, you are able to import all trees >with "treenames='*'". > >Please let me know if this could solve your problem. > >Best regards >Christian > > >On 8/27/10 3:35 PM, Mike Walter wrote: >> Hi all, >> >> I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. >> >> library(xps) >> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. >> exonlevel=rep((8192+1024),3) >> scheme="Scheme_HuGene10stv1r4_na30_hg19.root" >> gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) >> data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) >> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, >> exonlevel=exonlevel, verbose = FALSE) >> >> >> Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: >> >> data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", >> filedir = getwd(), tmpdir = "", update = FALSE, >> select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) >> >> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), >> tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) >> >> OR >> >> >> data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", >> method="quantile", select="pmonly", option="transcript:together:none", >> logbase="0", params=c(0.0), exonlevel=exonlevel) >> >> >> in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? >> >> Thank you very much. >> >> Best, >> Mike >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> i386-pc-mingw32 >> >> locale: >> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >> [5] LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] xps_1.6.4 >> >> loaded via a namespace (and not attached): >> [1] tools_2.10.1 >> >> >> >> >>
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Dear Mike, First, I am glad to hear that the stepwise approach did finally work. Thank you also for sending me the screenshot which repeats the following message many times: This error is symptomatic of a Tree created as a memory-resident Tree Instead of doing: TTree *T = new TTree(...); TFile *f = new TFile(...); you should do: TFile *f = new TFile(...); TTree *T = new TTree(...); Since I create always TFile first before creating new TTree(s) this means that for some reason the connection to TFile got lost so that the trees are kept in RAM. If you have only 6 trees this is no problem but with 324 trees you get this error message. Sadly, the beginning of the error messages are lost so that I do not know whether TFile was created or not. Thus, at the moment I have no idea what might be the reason for this problem and until now this error has never been reported. I would really appreciate if you could you try to run rma() with 'filename = "dataRMA"' instead of 'filename = "tmpdt_dataRMA"' and let me know if the problem remains. Best regards Christian On 8/30/10 1:23 PM, Mike Walter wrote: > Dear Christian, > > Thanks for your help. To answer your questions first: I normally use RGui and my disk space was ~100Gb. I also tried the add.data=FALSE option, without success. > > So I did RMA normalization with 6 arrays in RTerm as you proposed. This worked fine. So I just tried to run RMA on all arrays on RTerm. Here, I got thousands of error messages after the "compution common mean" step was finished for all arrays. After approx. 20min of error messages scrolling over my screen windows ended R, so I couldn't copy any output. I made a screenshot, which is attached (although it might not make it into the BioC list). > > Therefore, I tried the stepwise approach in RTerm. To my great surprise, now everything worked fine. There was no error when I started the quantile normlization with the same code as before (except the verbose=TRUE). The median polish afterwards also worked. The output of RTerm is pasted below. > > So again, thank you very much for your help. > > Kind regards, > > Mike > > >> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = $ > + tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = TRUE) > Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na="" 30_hg19.roo=""> t> in<read> mode... > Creating new file<f: auswertung="" genepi_combined="" quantile.root="">... > Opening file<f: auswertung="" genepi_combined="" bkgd_correct.root=""> in<read> mode... > > Preprocessing data using method<preprocess>... > Normalizing raw data... > normalizing data using method<quantile>... > setting selector mask for typepm<9216> > finished filling<324> arrays. > computing common mean... > finished filling<324> trees. > preprocessing finished. >> save.image("F:/Auswertung/GENEPI_combined/GENEPI_all_stepwise.RData") >> data.mp = summarize.rma(data.norm, filename = "medianpolish", filedir = getw$ > + update = FALSE, option = "transcript", exonlevel = exonlevel, xps.scheme =$ > Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na="" 30_hg19.roo=""> t> in<read> mode... > Creating new file<f: auswertung="" genepi_combined="" medianpolish.root="">... > Opening file<f: auswertung="" genepi_combined="" quantile.root=""> in<read> mode... > Preprocessing data using method<preprocess>... > Converting raw data to expression levels... > summarizing with<medianpolish>... > setting selector mask for typepm<9216> > setting selector mask for typepm<9216> > calculating expression for<28829> of<33664> units...Finished. > expression statistics: > minimal expression level is<3.11771> > maximal expression level is<20015.1> > preprocessing finished. > Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_na="" 30_hg19.roo=""> t> in<read> mode... > Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... > > Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... > > Exporting data from tree<*> to file<f: auswertung="" genepi_combined="" medianpolish=""> .txt>... > Reading entries from<hugene-1_0-st-v1.ann> ...Finished > <28829> of<28829> records exported. > > > > -----Urspr?ngliche Nachricht----- > Von: cstrato<cstrato at="" aon.at=""> > Gesendet: 27.08.2010 21:05:46 > An: Mike Walter<michael_walter at="" email.de=""> > Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps > >> Dear Mike, >> >> In case that your problem turns out to be a memory-related problem, you >> can use rma(...,add.data=FALSE,..), which will prevent filling slot >> "data" with the expression levels. You can then import all normalized >> data or parts thereof using "export.expr()" or "root.expr()", as the >> help files show. >> >> Thus you could first run rma and then import the results in a separate step: >> >> ## rma >>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", >> normalize=T, exonlevel=exonlevel, add.data=FALSE, verbose = TRUE) >> >> ## import subset of trees: >> ds<- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), >> treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", >> as.dataframe=TRUE) >> >> ## use subset of trees >>> sub.rma<- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", >> c("name1.mdp", "name2", etc)) >>> str(sub.rma) >> >> Maybe after starting a new R-session, you are able to import all trees >> with "treenames='*'". >> >> Please let me know if this could solve your problem. >> >> Best regards >> Christian >> >> >> On 8/27/10 3:35 PM, Mike Walter wrote: >>> Hi all, >>> >>> I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. >>> >>> library(xps) >>> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. >>> exonlevel=rep((8192+1024),3) >>> scheme="Scheme_HuGene10stv1r4_na30_hg19.root" >>> gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) >>> data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) >>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, >>> exonlevel=exonlevel, verbose = FALSE) >>> >>> >>> Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: >>> >>> data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", >>> filedir = getwd(), tmpdir = "", update = FALSE, >>> select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) >>> >>> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), >>> tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) >>> >>> OR >>> >>> >>> data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", >>> method="quantile", select="pmonly", option="transcript:together:none", >>> logbase="0", params=c(0.0), exonlevel=exonlevel) >>> >>> >>> in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? >>> >>> Thank you very much. >>> >>> Best, >>> Mike >>> >>>> sessionInfo() >>> R version 2.10.1 (2009-12-14) >>> i386-pc-mingw32 >>> >>> locale: >>> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >>> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >>> [5] LC_TIME=German_Germany.1252 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] xps_1.6.4 >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.10.1 >>> >>> >>> >>> >> >
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Hi Christian, Changing the name of the file into"dataRMA" didn't help. So I captured the beginning of the error message just after calculation of common mean finished. It says: SysError in <tfile::writebuffer>: error writing to file F:/Auswertung/GENEPI_combined/dataRMA.root (-1) (No space left on device) So it seems to be an storage problem. However, there are still 95Gb free on my hard disk (F:). The drive, where I run ROOT and R has approx. 11Gb free disk space. I will try another drive with more than 200Gb space and see if the error still occurs. Best, Mike -----Urspr?ngliche Nachricht----- Von: cstrato <cstrato at="" aon.at=""> Gesendet: 30.08.2010 21:37:44 An: Mike Walter <michael_walter at="" email.de=""> Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps >Dear Mike, > >First, I am glad to hear that the stepwise approach did finally work. > >Thank you also for sending me the screenshot which repeats the following >message many times: > >This error is symptomatic of a Tree created as a memory-resident Tree >Instead of doing: > TTree *T = new TTree(...); > TFile *f = new TFile(...); >you should do: > TFile *f = new TFile(...); > TTree *T = new TTree(...); > >Since I create always TFile first before creating new TTree(s) this >means that for some reason the connection to TFile got lost so that the >trees are kept in RAM. If you have only 6 trees this is no problem but >with 324 trees you get this error message. Sadly, the beginning of the >error messages are lost so that I do not know whether TFile was created >or not. > >Thus, at the moment I have no idea what might be the reason for this >problem and until now this error has never been reported. > >I would really appreciate if you could you try to run rma() with >'filename = "dataRMA"' instead of 'filename = "tmpdt_dataRMA"' and let >me know if the problem remains. > >Best regards >Christian > > >On 8/30/10 1:23 PM, Mike Walter wrote: >> Dear Christian, >> >> Thanks for your help. To answer your questions first: I normally use RGui and my disk space was ~100Gb. I also tried the add.data=FALSE option, without success. >> >> So I did RMA normalization with 6 arrays in RTerm as you proposed. This worked fine. So I just tried to run RMA on all arrays on RTerm. Here, I got thousands of error messages after the "compution common mean" step was finished for all arrays. After approx. 20min of error messages scrolling over my screen windows ended R, so I couldn't copy any output. I made a screenshot, which is attached (although it might not make it into the BioC list). >> >> Therefore, I tried the stepwise approach in RTerm. To my great surprise, now everything worked fine. There was no error when I started the quantile normlization with the same code as before (except the verbose=TRUE). The median polish afterwards also worked. The output of RTerm is pasted below. >> >> So again, thank you very much for your help. >> >> Kind regards, >> >> Mike >> >> >>> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = $ >> + tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = TRUE) >> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_n="" a30_hg19.roo="">> t> in<read> mode... >> Creating new file<f: auswertung="" genepi_combined="" quantile.root="">... >> Opening file<f: auswertung="" genepi_combined="" bkgd_correct.root=""> in<read> mode... >> >> Preprocessing data using method... >> Normalizing raw data... >> normalizing data using method... >> setting selector mask for typepm<9216> >> finished filling<324> arrays. >> computing common mean... >> finished filling<324> trees. >> preprocessing finished. >>> save.image("F:/Auswertung/GENEPI_combined/GENEPI_all_stepwise.RData") >>> data.mp = summarize.rma(data.norm, filename = "medianpolish", filedir = getw$ >> + update = FALSE, option = "transcript", exonlevel = exonlevel, xps.scheme =$ >> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_n="" a30_hg19.roo="">> t> in<read> mode... >> Creating new file<f: auswertung="" genepi_combined="" medianpolish.root="">... >> Opening file<f: auswertung="" genepi_combined="" quantile.root=""> in<read> mode... >> Preprocessing data using method... >> Converting raw data to expression levels... >> summarizing with<medianpolish>... >> setting selector mask for typepm<9216> >> setting selector mask for typepm<9216> >> calculating expression for<28829> of<33664> units...Finished. >> expression statistics: >> minimal expression level is<3.11771> >> maximal expression level is<20015.1> >> preprocessing finished. >> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_n="" a30_hg19.roo="">> t> in<read> mode... >> Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... >> >> Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... >> >> Exporting data from tree<*> to file<f: auswertung="" genepi_combined="" medianpolish="">> .txt>... >> Reading entries from<hugene-1_0-st-v1.ann> ...Finished >> <28829> of<28829> records exported. >> >> >> >> -----Urspr?ngliche Nachricht----- >> Von: cstrato<cstrato at="" aon.at=""> >> Gesendet: 27.08.2010 21:05:46 >> An: Mike Walter<michael_walter at="" email.de=""> >> Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps >> >>> Dear Mike, >>> >>> In case that your problem turns out to be a memory-related problem, you >>> can use rma(...,add.data=FALSE,..), which will prevent filling slot >>> "data" with the expression levels. You can then import all normalized >>> data or parts thereof using "export.expr()" or "root.expr()", as the >>> help files show. >>> >>> Thus you could first run rma and then import the results in a separate step: >>> >>> ## rma >>>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", >>> normalize=T, exonlevel=exonlevel, add.data=FALSE, verbose = TRUE) >>> >>> ## import subset of trees: >>> ds<- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), >>> treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", >>> as.dataframe=TRUE) >>> >>> ## use subset of trees >>>> sub.rma<- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", >>> c("name1.mdp", "name2", etc)) >>>> str(sub.rma) >>> >>> Maybe after starting a new R-session, you are able to import all trees >>> with "treenames='*'". >>> >>> Please let me know if this could solve your problem. >>> >>> Best regards >>> Christian >>> >>> >>> On 8/27/10 3:35 PM, Mike Walter wrote: >>>> Hi all, >>>> >>>> I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. >>>> >>>> library(xps) >>>> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. >>>> exonlevel=rep((8192+1024),3) >>>> scheme="Scheme_HuGene10stv1r4_na30_hg19.root" >>>> gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) >>>> data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) >>>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, >>>> exonlevel=exonlevel, verbose = FALSE) >>>> >>>> >>>> Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: >>>> >>>> data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", >>>> filedir = getwd(), tmpdir = "", update = FALSE, >>>> select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) >>>> >>>> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), >>>> tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) >>>> >>>> OR >>>> >>>> >>>> data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", >>>> method="quantile", select="pmonly", option="transcript:together:none", >>>> logbase="0", params=c(0.0), exonlevel=exonlevel) >>>> >>>> >>>> in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? >>>> >>>> Thank you very much. >>>> >>>> Best, >>>> Mike >>>> >>>>> sessionInfo() >>>> R version 2.10.1 (2009-12-14) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >>>> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >>>> [5] LC_TIME=German_Germany.1252 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] xps_1.6.4 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tools_2.10.1 >>>> >>>> >>>> >>>> >>> >
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Dear Mike, Thank you very much for your efforts. The error message explains the other error messages, because ROOT tries to create the trees in RAM since it can no longer write to the file. However, as you have 95GB free on your hard disk, it is not quite clear why the trees can no longer be written to the ROOT file. At the moment my only hint is that the hard disk could be too fragmented. In any case I will ask the ROOT developers if they have an explanation. Best regards Christian On 8/31/10 11:15 AM, Mike Walter wrote: > Hi Christian, > > Changing the name of the file into"dataRMA" didn't help. So I captured the beginning of the error message just after calculation of common mean finished. It says: > > SysError in<tfile::writebuffer>: error writing to file F:/Auswertung/GENEPI_combined/dataRMA.root (-1) (No space left on device) > > So it seems to be an storage problem. However, there are still 95Gb free on my hard disk (F:). The drive, where I run ROOT and R has approx. 11Gb free disk space. I will try another drive with more than 200Gb space and see if the error still occurs. > > Best, Mike > > -----Urspr?ngliche Nachricht----- > Von: cstrato<cstrato at="" aon.at=""> > Gesendet: 30.08.2010 21:37:44 > An: Mike Walter<michael_walter at="" email.de=""> > Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps > >> Dear Mike, >> >> First, I am glad to hear that the stepwise approach did finally work. >> >> Thank you also for sending me the screenshot which repeats the following >> message many times: >> >> This error is symptomatic of a Tree created as a memory-resident Tree >> Instead of doing: >> TTree *T = new TTree(...); >> TFile *f = new TFile(...); >> you should do: >> TFile *f = new TFile(...); >> TTree *T = new TTree(...); >> >> Since I create always TFile first before creating new TTree(s) this >> means that for some reason the connection to TFile got lost so that the >> trees are kept in RAM. If you have only 6 trees this is no problem but >> with 324 trees you get this error message. Sadly, the beginning of the >> error messages are lost so that I do not know whether TFile was created >> or not. >> >> Thus, at the moment I have no idea what might be the reason for this >> problem and until now this error has never been reported. >> >> I would really appreciate if you could you try to run rma() with >> 'filename = "dataRMA"' instead of 'filename = "tmpdt_dataRMA"' and let >> me know if the problem remains. >> >> Best regards >> Christian >> >> >> On 8/30/10 1:23 PM, Mike Walter wrote: >>> Dear Christian, >>> >>> Thanks for your help. To answer your questions first: I normally use RGui and my disk space was ~100Gb. I also tried the add.data=FALSE option, without success. >>> >>> So I did RMA normalization with 6 arrays in RTerm as you proposed. This worked fine. So I just tried to run RMA on all arrays on RTerm. Here, I got thousands of error messages after the "compution common mean" step was finished for all arrays. After approx. 20min of error messages scrolling over my screen windows ended R, so I couldn't copy any output. I made a screenshot, which is attached (although it might not make it into the BioC list). >>> >>> Therefore, I tried the stepwise approach in RTerm. To my great surprise, now everything worked fine. There was no error when I started the quantile normlization with the same code as before (except the verbose=TRUE). The median polish afterwards also worked. The output of RTerm is pasted below. >>> >>> So again, thank you very much for your help. >>> >>> Kind regards, >>> >>> Mike >>> >>> >>>> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = $ >>> + tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = TRUE) >>> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_="" na30_hg19.roo="">>> t> in<read> mode... >>> Creating new file<f: auswertung="" genepi_combined="" quantile.root="">... >>> Opening file<f: auswertung="" genepi_combined="" bkgd_correct.root=""> in<read> mode... >>> >>> Preprocessing data using method... >>> Normalizing raw data... >>> normalizing data using method... >>> setting selector mask for typepm<9216> >>> finished filling<324> arrays. >>> computing common mean... >>> finished filling<324> trees. >>> preprocessing finished. >>>> save.image("F:/Auswertung/GENEPI_combined/GENEPI_all_stepwise.RData") >>>> data.mp = summarize.rma(data.norm, filename = "medianpolish", filedir = getw$ >>> + update = FALSE, option = "transcript", exonlevel = exonlevel, xps.scheme =$ >>> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_="" na30_hg19.roo="">>> t> in<read> mode... >>> Creating new file<f: auswertung="" genepi_combined="" medianpolish.root="">... >>> Opening file<f: auswertung="" genepi_combined="" quantile.root=""> in<read> mode... >>> Preprocessing data using method... >>> Converting raw data to expression levels... >>> summarizing with<medianpolish>... >>> setting selector mask for typepm<9216> >>> setting selector mask for typepm<9216> >>> calculating expression for<28829> of<33664> units...Finished. >>> expression statistics: >>> minimal expression level is<3.11771> >>> maximal expression level is<20015.1> >>> preprocessing finished. >>> Opening file<x: affy="" qc_scripts="" xps="" schemes="" scheme_hugene10stv1r4_="" na30_hg19.roo="">>> t> in<read> mode... >>> Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... >>> >>> Opening file<f: auswertung="" genepi_combined="" medianpolish.root=""> in<read> mode... >>> >>> Exporting data from tree<*> to file<f: auswertung="" genepi_combined="" medianpolish="">>> .txt>... >>> Reading entries from<hugene-1_0-st-v1.ann> ...Finished >>> <28829> of<28829> records exported. >>> >>> >>> >>> -----Urspr?ngliche Nachricht----- >>> Von: cstrato<cstrato at="" aon.at=""> >>> Gesendet: 27.08.2010 21:05:46 >>> An: Mike Walter<michael_walter at="" email.de=""> >>> Betreff: Re: [BioC] Can't normalize 300+ HuGene arrays in xps >>> >>>> Dear Mike, >>>> >>>> In case that your problem turns out to be a memory-related problem, you >>>> can use rma(...,add.data=FALSE,..), which will prevent filling slot >>>> "data" with the expression levels. You can then import all normalized >>>> data or parts thereof using "export.expr()" or "root.expr()", as the >>>> help files show. >>>> >>>> Thus you could first run rma and then import the results in a separate step: >>>> >>>> ## rma >>>>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", >>>> normalize=T, exonlevel=exonlevel, add.data=FALSE, verbose = TRUE) >>>> >>>> ## import subset of trees: >>>> ds<- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), >>>> treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", >>>> as.dataframe=TRUE) >>>> >>>> ## use subset of trees >>>>> sub.rma<- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", >>>> c("name1.mdp", "name2", etc)) >>>>> str(sub.rma) >>>> >>>> Maybe after starting a new R-session, you are able to import all trees >>>> with "treenames='*'". >>>> >>>> Please let me know if this could solve your problem. >>>> >>>> Best regards >>>> Christian >>>> >>>> >>>> On 8/27/10 3:35 PM, Mike Walter wrote: >>>>> Hi all, >>>>> >>>>> I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes. >>>>> >>>>> library(xps) >>>>> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works. >>>>> exonlevel=rep((8192+1024),3) >>>>> scheme="Scheme_HuGene10stv1r4_na30_hg19.root" >>>>> gene.scheme<- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/")) >>>>> data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/")) >>>>> data.rma<- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, >>>>> exonlevel=exonlevel, verbose = FALSE) >>>>> >>>>> >>>>> Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization: >>>>> >>>>> data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", >>>>> filedir = getwd(), tmpdir = "", update = FALSE, >>>>> select = "antigenomic", exonlevel = exonlevel, verbose = FALSE) >>>>> >>>>> data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), >>>>> tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE) >>>>> >>>>> OR >>>>> >>>>> >>>>> data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", >>>>> method="quantile", select="pmonly", option="transcript:together:none", >>>>> logbase="0", params=c(0.0), exonlevel=exonlevel) >>>>> >>>>> >>>>> in both cases the output is "Fehler in .local(object, ...) : error in function ?Normalize?". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing? >>>>> >>>>> Thank you very much. >>>>> >>>>> Best, >>>>> Mike >>>>> >>>>>> sessionInfo() >>>>> R version 2.10.1 (2009-12-14) >>>>> i386-pc-mingw32 >>>>> >>>>> locale: >>>>> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 >>>>> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C >>>>> [5] LC_TIME=German_Germany.1252 >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods base >>>>> >>>>> other attached packages: >>>>> [1] xps_1.6.4 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] tools_2.10.1 >>>>> >>>>> >>>>> >>>>> >>>>> >
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