AgiMicroRna problems
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Mark Cowley ▴ 910
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Last seen 8.3 years ago
Dear Pedro, and BioCers similar to these 2 posts, i'm having problems running AgiMicroRna, because my Agilent TXT files are missing these three columns: gMeanSignal, gBGUsed, chr_coord. https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/03513 6.html http://comments.gmane.org/gmane.science.biology.informatics.conductor/ 28101 Here was my first attempt > library("AgiMicroRna") > targets.micro=readTargets(infile="/Volumes/****/projects/****/ targets.txt") (sorry - paranoid collaborator) > dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) Error in readGenericHeader(fullname, columns = columns, sep = sep) : Specified column headings not found in file I then tried to recreate my own readMicroRnaAFE which constructed dummy chr_coord, BGKus objects, but then I wasn't able to run the cvArray function: > library("AgiMicroRna") > targets.micro=readTargets(infile="/Volumes/external/projects/LW/ targets.txt") > dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) # QC plots ran OK > cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) Foreground: MeanSignal FILTERING BY ControlType FLAG RAW DATA: 15739 Error in object$other[[k]][i, , drop = FALSE] : incorrect number of dimensions > cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) Foreground: ProcessedSignal FILTERING BY ControlType FLAG RAW DATA: 15739 Error in object$other[[k]][i, , drop = FALSE] : incorrect number of dimensions I gave up on this approach, and instead I followed Pedro's advice in the first URL that I mentioned, and used gTotalSignal instead of gMeanSignal, and removed instances of chr_coord and gBGUsed, but then I can't get TGS, or RMA normalization to work > library("AgiMicroRna") > targets.micro=readTargets(infile="/Volumes/****/projects/****/ targets.txt") (sorry - paranoid collaborator) ddaux=read.maimages(files=targets.micro$FileName,source="agilent", + other.columns=list(IsGeneDetected="gIsGeneDetected", + IsSaturated ="gIsSaturated", + IsFeatNonUnifOF ="gIsFeatNonUnifOL", + IsFeatPopnOL ="gIsFeatPopnOL", + BGKmd ="gBGMedianSignal"), + columns=list(Rf="gTotalGeneSignal", + Gf="gTotalProbeSignal", + Rb="gTotalGeneSignal", + Gb="gProcessedSignal"), + verbose=TRUE,sep="\t",quote="") > ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, makePLOTpost = T, targets.micro, verbose = TRUE) Error in density.default(object[, n], na.rm = TRUE) : need at least 2 points to select a bandwidth automatically > > ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, makePLOTpost = F, targets.micro, verbose = TRUE) Error in xy.coords(x, y) : 'x' and 'y' lengths differ > > > ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) Error in split.default(0:(length(pNList) - 1), pNList) : Group length is 0 but data length > 0 # this takes quite a few minutes to process, then gives this error I've seen quite a bit of Agilent microRNA data through our centre, and can't recall ever seeing a chr_coord column, so is this to do with different versions of Agilent Feature Extraction, or different defaults set by the array facility? I'd really like to RMA normalize these data, so any help would be really appreciated cheers, Mark sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 locale: [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 limma_3.4.3 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 tools_2.11.1 > ----------------------------------------------------- Mark Cowley, PhD Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- [[alternative HTML version deleted]]
Normalization PROcess microRNA AgiMicroRna Normalization PROcess microRNA AgiMicroRna • 1.3k views
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Mark Cowley ▴ 910
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Last seen 8.3 years ago
Has anyone had success using AgiMicroRna recently? what array types were you using? cheers, Mark On 21/09/2010, at 9:44 PM, Mark Cowley wrote: > Dear Pedro, and BioCers > similar to these 2 posts, i'm having problems running AgiMicroRna, > because my Agilent TXT files are missing these three columns: > gMeanSignal, gBGUsed, chr_coord. > https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/035 136.html > http://comments.gmane.org/gmane.science.biology.informatics.conducto r/28101 > > Here was my first attempt >> library("AgiMicroRna") >> targets.micro=readTargets(infile="/Volumes/****/projects/****/ > targets.txt") (sorry - paranoid collaborator) >> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) > Error in readGenericHeader(fullname, columns = columns, sep = sep) : > Specified column headings not found in file > > I then tried to recreate my own readMicroRnaAFE which constructed > dummy chr_coord, BGKus objects, but then I wasn't able to run the > cvArray function: >> library("AgiMicroRna") >> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ > targets.txt") >> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) > # QC plots ran OK >> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) > Foreground: MeanSignal > > FILTERING BY ControlType FLAG > > RAW DATA: 15739 > Error in object$other[[k]][i, , drop = FALSE] : > incorrect number of dimensions >> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) > Foreground: ProcessedSignal > > FILTERING BY ControlType FLAG > > RAW DATA: 15739 > Error in object$other[[k]][i, , drop = FALSE] : > incorrect number of dimensions > > I gave up on this approach, and instead I followed Pedro's advice in > the first URL that I mentioned, and used gTotalSignal instead of > gMeanSignal, and removed instances of chr_coord and gBGUsed, but then > I can't get TGS, or RMA normalization to work > >> library("AgiMicroRna") >> targets.micro=readTargets(infile="/Volumes/****/projects/****/ > targets.txt") (sorry - paranoid collaborator) > ddaux=read.maimages(files=targets.micro$FileName,source="agilent", > + > other.columns=list(IsGeneDetected="gIsGeneDetected", > + > IsSaturated > ="gIsSaturated", > + > IsFeatNonUnifOF > ="gIsFeatNonUnifOL", > + > IsFeatPopnOL > ="gIsFeatPopnOL", > + > BGKmd > ="gBGMedianSignal"), > + columns=list(Rf="gTotalGeneSignal", > + > Gf="gTotalProbeSignal", > + > Rb="gTotalGeneSignal", > + > Gb="gProcessedSignal"), > + verbose=TRUE,sep="\t",quote="") >> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, > makePLOTpost = T, targets.micro, verbose = TRUE) > Error in density.default(object[, n], na.rm = TRUE) : > need at least 2 points to select a bandwidth automatically >> >> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, > makePLOTpost = F, targets.micro, verbose = TRUE) > Error in xy.coords(x, y) : 'x' and 'y' lengths differ >> >> >> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) > Error in split.default(0:(length(pNList) - 1), pNList) : > Group length is 0 but data length > 0 > # this takes quite a few minutes to process, then gives this error > > I've seen quite a bit of Agilent microRNA data through our centre, and > can't recall ever seeing a chr_coord column, so is this to do with > different versions of Agilent Feature Extraction, or different > defaults set by the array facility? > > I'd really like to RMA normalize these data, so any help would be > really appreciated > > cheers, > Mark > > > sessionInfo() > R version 2.11.1 (2010-05-31) > i386-apple-darwin9.8.0 > > locale: > [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 > limma_3.4.3 Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 tools_2.11.1 >> > > > ----------------------------------------------------- > Mark Cowley, PhD > > Peter Wills Bioinformatics Centre > Garvan Institute of Medical Research, Sydney, Australia > ----------------------------------------------------- > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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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Dear List, I am sure this has been discussed before in the list, so I would be happy even if someone points me to the right previous discussion. I have a Nimblegen gene expression dataset as .pairs file. Using dummy 2nd channel reading, I have managed to normalize this dataset (vsn normalization). lmFit also works with the normalized dataset. However, when I try to perform eBayes fit, I am hitting a snag. eBayes fit returns a lot of error at this last stage. I have given the steps / results from each step in this workflow. If someone has already faced this issue and resolved it - i would be happy to try it. Also, if there is a basic mistake I am making, can someone please let me know. Thanks. -- k. ===========================================================* > library(limma) > target=readTargets('list') > x=read.maimages(target$FileName,columns=list(R="PM",G="PM"),annotation =c("PROBE_ID","X","Y")) Read GSM519643.pair.val Read GSM519644.pair.val Read GSM519645.pair.val Read GSM519646.pair.val Read GSM519647.pair.val Read GSM519648.pair.val Read GSM519649.pair.val Read GSM519650.pair.val Read GSM519651.pair.val > x$R=NULL > xNorm=backgroundCorrect(x,method="normexp") > library(arrayQualityMetrics) Loading required package: affyPLM Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: gcrma Loading required package: preprocessCore Attaching package: 'affyPLM' The following object(s) are masked from package:stats : resid, residuals, weights > xEsetNorm=new("ExpressionSet",exprs=xNorm$G) > library(vsn) > xEsetVsn=vsn(xEsetNorm) Note: The function 'vsn' has been superseded by 'vsn2'. The function 'vsn' remains in the package for backward compatibility, but for new projects, please use 'vsn2'. vsn: 389307 x 9 matrix (1 stratum). 100% done. > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,)) + ) Error in factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3, )) : element 9 is empty; the part of the args list of 'c' being evaluated was: (1, 1, 2, 2, 2, 3, 3, 3, ) > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) > colnames(design)=c('Ctrl','Chlr1','Chlr2') > design Ctrl Chlr1 Chlr2 1 1 0 0 2 1 0 0 3 1 0 0 4 0 1 0 5 0 1 0 6 0 1 0 7 0 0 1 8 0 0 1 9 0 0 1 attr(,"assign") [1] 1 1 1 attr(,"contrasts") attr(,"contrasts")$`factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3))` [1] "contr.treatment" > xFit=lmFit(xEsetVsn,design) > contmat=makeContrasts(Chlr1-Ctrl,Chlr2-Ctrl,levels=design) > contmat Contrasts Levels Chlr1 - Ctrl Chlr2 - Ctrl Ctrl -1 -1 Chlr1 1 0 Chlr2 0 1 > xFit2=eBayes(xFit xFit > xFit2=eBayes(xFit,contmat) Error in log(proportion/(1 - proportion)) - log(r)/2 : non-conformable arrays In addition: Warning messages: 1: In if (ntarget < 1) return(NA) : the condition has length > 1 and only the first element will be used 2: In if (ntarget < 1) return(NA) : the condition has length > 1 and only the first element will be used 3: In if (ntarget < 1) return(NA) : the condition has length > 1 and only the first element will be used 4: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim) : Estimation of var.prior failed - set to default value 5: In log(proportion/(1 - proportion)) : NaNs produced *===================================================================== ==== -- ======================================= From Ignorance to Truth, From Darkness to Light, From Mortality to Immortality ... ======================================= [[alternative HTML version deleted]]
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Hi Karthi, On 9/29/2010 3:19 AM, Karthi Sivaraman wrote: > Dear List, > > I am sure this has been discussed before in the list, so I would be > happy even if someone points me to the right previous discussion. > > I have a Nimblegen gene expression dataset as .pairs file. Using dummy > 2nd channel reading, I have managed to normalize this dataset (vsn > normalization). lmFit also works with the normalized dataset. However, > when I try to perform eBayes fit, I am hitting a snag. eBayes fit > returns a lot of error at this last stage. > > I have given the steps / results from each step in this workflow. If > someone has already faced this issue and resolved it - i would be happy > to try it. Also, if there is a basic mistake I am making, can someone > please let me know. Thanks. -- k. > ===========================================================* > > library(limma) > > target=readTargets('list') > > > x=read.maimages(target$FileName,columns=list(R="PM",G="PM"),annotati on=c("PROBE_ID","X","Y")) > Read GSM519643.pair.val > Read GSM519644.pair.val > Read GSM519645.pair.val > Read GSM519646.pair.val > Read GSM519647.pair.val > Read GSM519648.pair.val > Read GSM519649.pair.val > Read GSM519650.pair.val > Read GSM519651.pair.val > > x$R=NULL > > xNorm=backgroundCorrect(x,method="normexp") > > library(arrayQualityMetrics) > Loading required package: affyPLM > Loading required package: affy > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: gcrma > Loading required package: preprocessCore > > Attaching package: 'affyPLM' > > > The following object(s) are masked from package:stats : > > resid, > residuals, > weights > > > xEsetNorm=new("ExpressionSet",exprs=xNorm$G) > > library(vsn) > > xEsetVsn=vsn(xEsetNorm) > Note: > The function 'vsn' has been superseded by 'vsn2'. > The function 'vsn' remains in the package for backward compatibility, > but for new projects, please use 'vsn2'. You might read (and follow) the note... > > vsn: 389307 x 9 matrix (1 stratum). 100% done. > > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,)) > + ) > Error in factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3, )) : > element 9 is empty; > the part of the args list of 'c' being evaluated was: > (1, 1, 2, 2, 2, 3, 3, 3, ) > > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) > > colnames(design)=c('Ctrl','Chlr1','Chlr2') > > design > Ctrl Chlr1 Chlr2 > 1 1 0 0 > 2 1 0 0 > 3 1 0 0 > 4 0 1 0 > 5 0 1 0 > 6 0 1 0 > 7 0 0 1 > 8 0 0 1 > 9 0 0 1 > attr(,"assign") > [1] 1 1 1 > attr(,"contrasts") > attr(,"contrasts")$`factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3))` > [1] "contr.treatment" > > > xFit=lmFit(xEsetVsn,design) > > contmat=makeContrasts(Chlr1-Ctrl,Chlr2-Ctrl,levels=design) > > contmat > Contrasts > Levels Chlr1 - Ctrl Chlr2 - Ctrl > Ctrl -1 -1 > Chlr1 1 0 > Chlr2 0 1 > > xFit2=eBayes(xFit > xFit > > xFit2=eBayes(xFit,contmat) There are no arguments for eBayes() that take a contrasts matrix, so I am not sure what you are trying to do here. You want to do the usual: xFit2 <- contrasts.fit(xFit, contmat) xFit2 <- eBayes(xFit2) Best, Jim > Error in log(proportion/(1 - proportion)) - log(r)/2 : > non-conformable arrays > In addition: Warning messages: > 1: In if (ntarget< 1) return(NA) : > the condition has length> 1 and only the first element will be used > 2: In if (ntarget< 1) return(NA) : > the condition has length> 1 and only the first element will be used > 3: In if (ntarget< 1) return(NA) : > the condition has length> 1 and only the first element will be used > 4: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = > stdev.coef.lim) : > Estimation of var.prior failed - set to default value > 5: In log(proportion/(1 - proportion)) : NaNs produced > *=================================================================== ====== > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Dear Jim, Thanks for pointing out the silly mistake. Sorry for the trouble. Thanks. Warm regards, k On 29/09/2010 21:14, James W. MacDonald wrote: > Hi Karthi, > > On 9/29/2010 3:19 AM, Karthi Sivaraman wrote: >> Dear List, >> >> I am sure this has been discussed before in the list, so I would be >> happy even if someone points me to the right previous discussion. >> >> I have a Nimblegen gene expression dataset as .pairs file. Using dummy >> 2nd channel reading, I have managed to normalize this dataset (vsn >> normalization). lmFit also works with the normalized dataset. However, >> when I try to perform eBayes fit, I am hitting a snag. eBayes fit >> returns a lot of error at this last stage. >> >> I have given the steps / results from each step in this workflow. If >> someone has already faced this issue and resolved it - i would be happy >> to try it. Also, if there is a basic mistake I am making, can someone >> please let me know. Thanks. -- k. >> ===========================================================* >> > library(limma) >> > target=readTargets('list') >> > >> x=read.maimages(target$FileName,columns=list(R="PM",G="PM"),annotat ion=c("PROBE_ID","X","Y")) >> >> Read GSM519643.pair.val >> Read GSM519644.pair.val >> Read GSM519645.pair.val >> Read GSM519646.pair.val >> Read GSM519647.pair.val >> Read GSM519648.pair.val >> Read GSM519649.pair.val >> Read GSM519650.pair.val >> Read GSM519651.pair.val >> > x$R=NULL >> > xNorm=backgroundCorrect(x,method="normexp") >> > library(arrayQualityMetrics) >> Loading required package: affyPLM >> Loading required package: affy >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: gcrma >> Loading required package: preprocessCore >> >> Attaching package: 'affyPLM' >> >> >> The following object(s) are masked from package:stats : >> >> resid, >> residuals, >> weights >> >> > xEsetNorm=new("ExpressionSet",exprs=xNorm$G) >> > library(vsn) >> > xEsetVsn=vsn(xEsetNorm) >> Note: >> The function 'vsn' has been superseded by 'vsn2'. >> The function 'vsn' remains in the package for backward compatibility, >> but for new projects, please use 'vsn2'. > > You might read (and follow) the note... > >> >> vsn: 389307 x 9 matrix (1 stratum). 100% done. >> > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,)) >> + ) >> Error in factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3, )) : >> element 9 is empty; >> the part of the args list of 'c' being evaluated was: >> (1, 1, 2, 2, 2, 3, 3, 3, ) >> > design=model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3))) >> > colnames(design)=c('Ctrl','Chlr1','Chlr2') >> > design >> Ctrl Chlr1 Chlr2 >> 1 1 0 0 >> 2 1 0 0 >> 3 1 0 0 >> 4 0 1 0 >> 5 0 1 0 >> 6 0 1 0 >> 7 0 0 1 >> 8 0 0 1 >> 9 0 0 1 >> attr(,"assign") >> [1] 1 1 1 >> attr(,"contrasts") >> attr(,"contrasts")$`factor(c(1, 1, 1, 2, 2, 2, 3, 3, 3))` >> [1] "contr.treatment" >> >> > xFit=lmFit(xEsetVsn,design) >> > contmat=makeContrasts(Chlr1-Ctrl,Chlr2-Ctrl,levels=design) >> > contmat >> Contrasts >> Levels Chlr1 - Ctrl Chlr2 - Ctrl >> Ctrl -1 -1 >> Chlr1 1 0 >> Chlr2 0 1 >> > xFit2=eBayes(xFit >> xFit >> > xFit2=eBayes(xFit,contmat) > > There are no arguments for eBayes() that take a contrasts matrix, so I > am not sure what you are trying to do here. You want to do the usual: > > xFit2 <- contrasts.fit(xFit, contmat) > xFit2 <- eBayes(xFit2) > > Best, > > Jim > > > >> Error in log(proportion/(1 - proportion)) - log(r)/2 : >> non-conformable arrays >> In addition: Warning messages: >> 1: In if (ntarget< 1) return(NA) : >> the condition has length> 1 and only the first element will be used >> 2: In if (ntarget< 1) return(NA) : >> the condition has length> 1 and only the first element will be used >> 3: In if (ntarget< 1) return(NA) : >> the condition has length> 1 and only the first element will be used >> 4: In ebayes(fit = fit, proportion = proportion, stdev.coef.lim = >> stdev.coef.lim) : >> Estimation of var.prior failed - set to default value >> 5: In log(proportion/(1 - proportion)) : NaNs produced >> *================================================================== ======= >> >> > -- ======================================= From Ignorance to Truth, From Darkness to Light, From Mortality to Immortality ...
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Hi Mark, I just received a data set of Human miRNA V3 and AgiMicroRna does not work. Basically the column gMeanSignal, gBGUsed, chr_coord are not present. I modified readMicroRnaAFE accordingly to the post of Pedro (see after the text) My question is why those columns are not present in the txt file. In the folder I received from our facility there is a XML file containing the settings of the FeatureExtraction software. One flag is TextOutPkgType="Compact" Is there a way to test if this option can be change and what is the effect on the txt output? readMicroRnaAFE <- function (targets, verbose = FALSE) { if (!is(targets, "data.frame")) { stop("'targets' must be a data.frame") } ddaux=read.maimages(files=targets$FileName,source="agilent", other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated ="gIsSaturated", IsFeatNonUnifOF ="gIsFeatNonUnifOL", IsFeatPopnOL ="gIsFeatPopnOL", BGKmd ="gBGMedianSignal"), columns=list(R="gTotalGeneSignal", G="gTotalProbeSignal", Rb="gTotalGeneSignal", Gb="gProcessedSignal"), verbose=TRUE,sep="\t",quote="" ) #return(ddaux) dd = new("RGList") dd$R = ddaux$R dd$G = ddaux$G dd$Rb = ddaux$Rb dd$Gb = ddaux$Gb dd$targets = ddaux$targets ## suppress column 6 that should have contain chr_pos I guess dd$genes = ddaux$genes[, c(4, 5)] dd$other = ddaux$other rm(ddaux) if (verbose) { cat("", "\n") cat(" RGList:", "\n") cat("\tdd$R:\t\t'gTotalGeneSignal' ", "\n") cat("\tdd$G:\t\t'gTotalProbeSignal' ", "\n") cat("\tdd$Rb:\t\t'gMeanSignal' ", "\n") cat("\tdd$Gb:\t\t'gProcessedSignal' ", "\n") cat("", "\n") } return(dd) } David On Sep 28, 2010, at 11:52 PM, Mark Cowley wrote: > Has anyone had success using AgiMicroRna recently? what array types were you using? > cheers, > Mark > > On 21/09/2010, at 9:44 PM, Mark Cowley wrote: > >> Dear Pedro, and BioCers >> similar to these 2 posts, i'm having problems running AgiMicroRna, >> because my Agilent TXT files are missing these three columns: >> gMeanSignal, gBGUsed, chr_coord. >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/03 5136.html >> http://comments.gmane.org/gmane.science.biology.informatics.conduct or/28101 >> >> Here was my first attempt >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >> targets.txt") (sorry - paranoid collaborator) >>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >> Specified column headings not found in file >> >> I then tried to recreate my own readMicroRnaAFE which constructed >> dummy chr_coord, BGKus objects, but then I wasn't able to run the >> cvArray function: >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ >> targets.txt") >>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >> # QC plots ran OK >>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) >> Foreground: MeanSignal >> >> FILTERING BY ControlType FLAG >> >> RAW DATA: 15739 >> Error in object$other[[k]][i, , drop = FALSE] : >> incorrect number of dimensions >>> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) >> Foreground: ProcessedSignal >> >> FILTERING BY ControlType FLAG >> >> RAW DATA: 15739 >> Error in object$other[[k]][i, , drop = FALSE] : >> incorrect number of dimensions >> >> I gave up on this approach, and instead I followed Pedro's advice in >> the first URL that I mentioned, and used gTotalSignal instead of >> gMeanSignal, and removed instances of chr_coord and gBGUsed, but then >> I can't get TGS, or RMA normalization to work >> >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >> targets.txt") (sorry - paranoid collaborator) >> ddaux=read.maimages(files=targets.micro$FileName,source="agilent", >> + >> other.columns=list(IsGeneDetected="gIsGeneDetected", >> + >> IsSaturated >> ="gIsSaturated", >> + >> IsFeatNonUnifOF >> ="gIsFeatNonUnifOL", >> + >> IsFeatPopnOL >> ="gIsFeatPopnOL", >> + >> BGKmd >> ="gBGMedianSignal"), >> + columns=list(Rf="gTotalGeneSignal", >> + >> Gf="gTotalProbeSignal", >> + >> Rb="gTotalGeneSignal", >> + >> Gb="gProcessedSignal"), >> + verbose=TRUE,sep="\t",quote="") >>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, >> makePLOTpost = T, targets.micro, verbose = TRUE) >> Error in density.default(object[, n], na.rm = TRUE) : >> need at least 2 points to select a bandwidth automatically >>> >>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, >> makePLOTpost = F, targets.micro, verbose = TRUE) >> Error in xy.coords(x, y) : 'x' and 'y' lengths differ >>> >>> >>> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) >> Error in split.default(0:(length(pNList) - 1), pNList) : >> Group length is 0 but data length > 0 >> # this takes quite a few minutes to process, then gives this error >> >> I've seen quite a bit of Agilent microRNA data through our centre, and >> can't recall ever seeing a chr_coord column, so is this to do with >> different versions of Agilent Feature Extraction, or different >> defaults set by the array facility? >> >> I'd really like to RMA normalize these data, so any help would be >> really appreciated >> >> cheers, >> Mark >> >> >> sessionInfo() >> R version 2.11.1 (2010-05-31) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >> limma_3.4.3 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 tools_2.11.1 >>> >> >> >> ----------------------------------------------------- >> Mark Cowley, PhD >> >> Peter Wills Bioinformatics Centre >> Garvan Institute of Medical Research, Sydney, Australia >> ----------------------------------------------------- >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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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Thanks for your inpiut David, Perhaps there was something that I overlooked in Pedro's original post, so i'll certainly try your attached function. cheers, Mark On 30/09/2010, at 4:01 AM, David Ruau wrote: > Hi Mark, > > I just received a data set of Human miRNA V3 and AgiMicroRna does > not work. > Basically the column gMeanSignal, gBGUsed, chr_coord are not present. > I modified readMicroRnaAFE accordingly to the post of Pedro (see > after the text) > > My question is why those columns are not present in the txt file. > In the folder I received from our facility there is a XML file > containing the settings of the FeatureExtraction software. One flag > is TextOutPkgType="Compact" > Is there a way to test if this option can be change and what is the > effect on the txt output? > > readMicroRnaAFE <- function (targets, verbose = FALSE) > { > if (!is(targets, "data.frame")) { > stop("'targets' must be a data.frame") > } > ddaux=read.maimages(files=targets$FileName,source="agilent", > other.columns=list(IsGeneDetected="gIsGeneDetected", > IsSaturated ="gIsSaturated", IsFeatNonUnifOF ="gIsFeatNonUnifOL", > IsFeatPopnOL ="gIsFeatPopnOL", BGKmd ="gBGMedianSignal"), > columns=list(R="gTotalGeneSignal", G="gTotalProbeSignal", > Rb="gTotalGeneSignal", Gb="gProcessedSignal"), > verbose=TRUE,sep="\t",quote="" > ) > #return(ddaux) > dd = new("RGList") > dd$R = ddaux$R > dd$G = ddaux$G > dd$Rb = ddaux$Rb > dd$Gb = ddaux$Gb > dd$targets = ddaux$targets > ## suppress column 6 that should have contain chr_pos I guess > dd$genes = ddaux$genes[, c(4, 5)] > dd$other = ddaux$other > rm(ddaux) > if (verbose) { > cat("", "\n") > cat(" RGList:", "\n") > cat("\tdd$R:\t\t'gTotalGeneSignal' ", "\n") > cat("\tdd$G:\t\t'gTotalProbeSignal' ", "\n") > cat("\tdd$Rb:\t\t'gMeanSignal' ", "\n") > cat("\tdd$Gb:\t\t'gProcessedSignal' ", "\n") > cat("", "\n") > } > return(dd) > } > > > David > > On Sep 28, 2010, at 11:52 PM, Mark Cowley wrote: > >> Has anyone had success using AgiMicroRna recently? what array types >> were you using? >> cheers, >> Mark >> >> On 21/09/2010, at 9:44 PM, Mark Cowley wrote: >> >>> Dear Pedro, and BioCers >>> similar to these 2 posts, i'm having problems running AgiMicroRna, >>> because my Agilent TXT files are missing these three columns: >>> gMeanSignal, gBGUsed, chr_coord. >>> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/0 35136.html >>> http://comments.gmane.org/gmane.science.biology.informatics.conduc tor/28101 >>> >>> Here was my first attempt >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >>> targets.txt") (sorry - paranoid collaborator) >>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >>> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >>> Specified column headings not found in file >>> >>> I then tried to recreate my own readMicroRnaAFE which constructed >>> dummy chr_coord, BGKus objects, but then I wasn't able to run the >>> cvArray function: >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ >>> targets.txt") >>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >>> # QC plots ran OK >>>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) >>> Foreground: MeanSignal >>> >>> FILTERING BY ControlType FLAG >>> >>> RAW DATA: 15739 >>> Error in object$other[[k]][i, , drop = FALSE] : >>> incorrect number of dimensions >>>> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) >>> Foreground: ProcessedSignal >>> >>> FILTERING BY ControlType FLAG >>> >>> RAW DATA: 15739 >>> Error in object$other[[k]][i, , drop = FALSE] : >>> incorrect number of dimensions >>> >>> I gave up on this approach, and instead I followed Pedro's advice in >>> the first URL that I mentioned, and used gTotalSignal instead of >>> gMeanSignal, and removed instances of chr_coord and gBGUsed, but >>> then >>> I can't get TGS, or RMA normalization to work >>> >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >>> targets.txt") (sorry - paranoid collaborator) >>> ddaux=read.maimages(files=targets.micro$FileName,source="agilent", >>> + >>> other.columns=list(IsGeneDetected="gIsGeneDetected", >>> + >>> IsSaturated >>> ="gIsSaturated", >>> + >>> IsFeatNonUnifOF >>> ="gIsFeatNonUnifOL", >>> + >>> IsFeatPopnOL >>> ="gIsFeatPopnOL", >>> + >>> BGKmd >>> ="gBGMedianSignal"), >>> + columns=list(Rf="gTotalGeneSignal", >>> + >>> Gf="gTotalProbeSignal", >>> + >>> Rb="gTotalGeneSignal", >>> + >>> Gb="gProcessedSignal"), >>> + verbose=TRUE,sep="\t",quote="") >>>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, >>> makePLOTpost = T, targets.micro, verbose = TRUE) >>> Error in density.default(object[, n], na.rm = TRUE) : >>> need at least 2 points to select a bandwidth automatically >>>> >>>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, >>> makePLOTpost = F, targets.micro, verbose = TRUE) >>> Error in xy.coords(x, y) : 'x' and 'y' lengths differ >>>> >>>> >>>> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) >>> Error in split.default(0:(length(pNList) - 1), pNList) : >>> Group length is 0 but data length > 0 >>> # this takes quite a few minutes to process, then gives this error >>> >>> I've seen quite a bit of Agilent microRNA data through our centre, >>> and >>> can't recall ever seeing a chr_coord column, so is this to do with >>> different versions of Agilent Feature Extraction, or different >>> defaults set by the array facility? >>> >>> I'd really like to RMA normalize these data, so any help would be >>> really appreciated >>> >>> cheers, >>> Mark >>> >>> >>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> i386-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >>> limma_3.4.3 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 tools_2.11.1 >>>> >>> >>> >>> ----------------------------------------------------- >>> Mark Cowley, PhD >>> >>> Peter Wills Bioinformatics Centre >>> Garvan Institute of Medical Research, Sydney, Australia >>> ----------------------------------------------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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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Hi, If the data is extracted with the FE report set to 'Full' rather than 'Compact', then it reports the gMeanSignal and gBGUsed (but not chr_coord). You can then follow the package using the amendments Pedro posted to get around not having the chr_coord column. Cheers, Corrinne -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of David Ruau Sent: 29 September 2010 19:02 To: Mark Cowley Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] AgiMicroRna problems Hi Mark, I just received a data set of Human miRNA V3 and AgiMicroRna does not work. Basically the column gMeanSignal, gBGUsed, chr_coord are not present. I modified readMicroRnaAFE accordingly to the post of Pedro (see after the text) My question is why those columns are not present in the txt file. In the folder I received from our facility there is a XML file containing the settings of the FeatureExtraction software. One flag is TextOutPkgType="Compact" Is there a way to test if this option can be change and what is the effect on the txt output? readMicroRnaAFE <- function (targets, verbose = FALSE) { if (!is(targets, "data.frame")) { stop("'targets' must be a data.frame") } ddaux=read.maimages(files=targets$FileName,source="agilent", other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated ="gIsSaturated", IsFeatNonUnifOF ="gIsFeatNonUnifOL", IsFeatPopnOL ="gIsFeatPopnOL", BGKmd ="gBGMedianSignal"), columns=list(R="gTotalGeneSignal", G="gTotalProbeSignal", Rb="gTotalGeneSignal", Gb="gProcessedSignal"), verbose=TRUE,sep="\t",quote="" ) #return(ddaux) dd = new("RGList") dd$R = ddaux$R dd$G = ddaux$G dd$Rb = ddaux$Rb dd$Gb = ddaux$Gb dd$targets = ddaux$targets ## suppress column 6 that should have contain chr_pos I guess dd$genes = ddaux$genes[, c(4, 5)] dd$other = ddaux$other rm(ddaux) if (verbose) { cat("", "\n") cat(" RGList:", "\n") cat("\tdd$R:\t\t'gTotalGeneSignal' ", "\n") cat("\tdd$G:\t\t'gTotalProbeSignal' ", "\n") cat("\tdd$Rb:\t\t'gMeanSignal' ", "\n") cat("\tdd$Gb:\t\t'gProcessedSignal' ", "\n") cat("", "\n") } return(dd) } David On Sep 28, 2010, at 11:52 PM, Mark Cowley wrote: > Has anyone had success using AgiMicroRna recently? what array types were you using? > cheers, > Mark > > On 21/09/2010, at 9:44 PM, Mark Cowley wrote: > >> Dear Pedro, and BioCers >> similar to these 2 posts, i'm having problems running AgiMicroRna, >> because my Agilent TXT files are missing these three columns: >> gMeanSignal, gBGUsed, chr_coord. >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/03 5136.html >> http://comments.gmane.org/gmane.science.biology.informatics.conduct or/28101 >> >> Here was my first attempt >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >> targets.txt") (sorry - paranoid collaborator) >>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >> Specified column headings not found in file >> >> I then tried to recreate my own readMicroRnaAFE which constructed >> dummy chr_coord, BGKus objects, but then I wasn't able to run the >> cvArray function: >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ >> targets.txt") >>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >> # QC plots ran OK >>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) >> Foreground: MeanSignal >> >> FILTERING BY ControlType FLAG >> >> RAW DATA: 15739 >> Error in object$other[[k]][i, , drop = FALSE] : >> incorrect number of dimensions >>> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) >> Foreground: ProcessedSignal >> >> FILTERING BY ControlType FLAG >> >> RAW DATA: 15739 >> Error in object$other[[k]][i, , drop = FALSE] : >> incorrect number of dimensions >> >> I gave up on this approach, and instead I followed Pedro's advice in >> the first URL that I mentioned, and used gTotalSignal instead of >> gMeanSignal, and removed instances of chr_coord and gBGUsed, but then >> I can't get TGS, or RMA normalization to work >> >>> library("AgiMicroRna") >>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >> targets.txt") (sorry - paranoid collaborator) >> ddaux=read.maimages(files=targets.micro$FileName,source="agilent", >> + >> other.columns=list(IsGeneDetected="gIsGeneDetected", >> + >> IsSaturated >> ="gIsSaturated", >> + >> IsFeatNonUnifOF >> ="gIsFeatNonUnifOL", >> + >> IsFeatPopnOL >> ="gIsFeatPopnOL", >> + >> BGKmd >> ="gBGMedianSignal"), >> + columns=list(Rf="gTotalGeneSignal", >> + >> Gf="gTotalProbeSignal", >> + >> Rb="gTotalGeneSignal", >> + >> Gb="gProcessedSignal"), >> + verbose=TRUE,sep="\t",quote="") >>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, >> makePLOTpost = T, targets.micro, verbose = TRUE) >> Error in density.default(object[, n], na.rm = TRUE) : >> need at least 2 points to select a bandwidth automatically >>> >>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, >> makePLOTpost = F, targets.micro, verbose = TRUE) >> Error in xy.coords(x, y) : 'x' and 'y' lengths differ >>> >>> >>> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) >> Error in split.default(0:(length(pNList) - 1), pNList) : >> Group length is 0 but data length > 0 >> # this takes quite a few minutes to process, then gives this error >> >> I've seen quite a bit of Agilent microRNA data through our centre, and >> can't recall ever seeing a chr_coord column, so is this to do with >> different versions of Agilent Feature Extraction, or different >> defaults set by the array facility? >> >> I'd really like to RMA normalize these data, so any help would be >> really appreciated >> >> cheers, >> Mark >> >> >> sessionInfo() >> R version 2.11.1 (2010-05-31) >> i386-apple-darwin9.8.0 >> >> locale: >> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >> limma_3.4.3 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.16.0 tools_2.11.1 >>> >> >> >> ----------------------------------------------------- >> Mark Cowley, PhD >> >> Peter Wills Bioinformatics Centre >> Garvan Institute of Medical Research, Sydney, Australia >> ----------------------------------------------------- >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 _______________________________________________ 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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Hi, I wonder if our core facility even knows about that option! Thanks for bringing this up cheers, mark On 30/09/2010, at 11:57 PM, Segal, Corrinne wrote: > Hi, > > If the data is extracted with the FE report set to 'Full' rather > than 'Compact', then it reports the gMeanSignal and gBGUsed (but not > chr_coord). You can then follow the package using the amendments > Pedro posted to get around not having the chr_coord column. > > Cheers, > > Corrinne > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto :bioconductor-bounces at stat.math.ethz.ch > ] On Behalf Of David Ruau > Sent: 29 September 2010 19:02 > To: Mark Cowley > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] AgiMicroRna problems > > Hi Mark, > > I just received a data set of Human miRNA V3 and AgiMicroRna does > not work. > Basically the column gMeanSignal, gBGUsed, chr_coord are not present. > I modified readMicroRnaAFE accordingly to the post of Pedro (see > after the text) > > My question is why those columns are not present in the txt file. > In the folder I received from our facility there is a XML file > containing the settings of the FeatureExtraction software. One flag > is TextOutPkgType="Compact" > Is there a way to test if this option can be change and what is the > effect on the txt output? > > readMicroRnaAFE <- function (targets, verbose = FALSE) > { > if (!is(targets, "data.frame")) { > stop("'targets' must be a data.frame") > } > ddaux=read.maimages(files=targets$FileName,source="agilent", > other.columns=list(IsGeneDetected="gIsGeneDetected", > IsSaturated ="gIsSaturated", IsFeatNonUnifOF ="gIsFeatNonUnifOL", > IsFeatPopnOL ="gIsFeatPopnOL", BGKmd ="gBGMedianSignal"), > columns=list(R="gTotalGeneSignal", G="gTotalProbeSignal", > Rb="gTotalGeneSignal", Gb="gProcessedSignal"), > verbose=TRUE,sep="\t",quote="" > ) > #return(ddaux) > dd = new("RGList") > dd$R = ddaux$R > dd$G = ddaux$G > dd$Rb = ddaux$Rb > dd$Gb = ddaux$Gb > dd$targets = ddaux$targets > ## suppress column 6 that should have contain chr_pos I guess > dd$genes = ddaux$genes[, c(4, 5)] > dd$other = ddaux$other > rm(ddaux) > if (verbose) { > cat("", "\n") > cat(" RGList:", "\n") > cat("\tdd$R:\t\t'gTotalGeneSignal' ", "\n") > cat("\tdd$G:\t\t'gTotalProbeSignal' ", "\n") > cat("\tdd$Rb:\t\t'gMeanSignal' ", "\n") > cat("\tdd$Gb:\t\t'gProcessedSignal' ", "\n") > cat("", "\n") > } > return(dd) > } > > > David > > On Sep 28, 2010, at 11:52 PM, Mark Cowley wrote: > >> Has anyone had success using AgiMicroRna recently? what array types >> were you using? >> cheers, >> Mark >> >> On 21/09/2010, at 9:44 PM, Mark Cowley wrote: >> >>> Dear Pedro, and BioCers >>> similar to these 2 posts, i'm having problems running AgiMicroRna, >>> because my Agilent TXT files are missing these three columns: >>> gMeanSignal, gBGUsed, chr_coord. >>> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-August/0 35136.html >>> http://comments.gmane.org/gmane.science.biology.informatics.conduc tor/28101 >>> >>> Here was my first attempt >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >>> targets.txt") (sorry - paranoid collaborator) >>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >>> Error in readGenericHeader(fullname, columns = columns, sep = sep) : >>> Specified column headings not found in file >>> >>> I then tried to recreate my own readMicroRnaAFE which constructed >>> dummy chr_coord, BGKus objects, but then I wasn't able to run the >>> cvArray function: >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/external/projects/LW/ >>> targets.txt") >>>> dd.micro=readMicroRnaAFE(targets.micro,verbose=TRUE) >>> # QC plots ran OK >>>> cvArray(dd.micro,"MeanSignal",targets.micro,verbose=TRUE) >>> Foreground: MeanSignal >>> >>> FILTERING BY ControlType FLAG >>> >>> RAW DATA: 15739 >>> Error in object$other[[k]][i, , drop = FALSE] : >>> incorrect number of dimensions >>>> cvArray(dd.micro,"ProcessedSignal",targets.micro,verbose=TRUE) >>> Foreground: ProcessedSignal >>> >>> FILTERING BY ControlType FLAG >>> >>> RAW DATA: 15739 >>> Error in object$other[[k]][i, , drop = FALSE] : >>> incorrect number of dimensions >>> >>> I gave up on this approach, and instead I followed Pedro's advice in >>> the first URL that I mentioned, and used gTotalSignal instead of >>> gMeanSignal, and removed instances of chr_coord and gBGUsed, but >>> then >>> I can't get TGS, or RMA normalization to work >>> >>>> library("AgiMicroRna") >>>> targets.micro=readTargets(infile="/Volumes/****/projects/****/ >>> targets.txt") (sorry - paranoid collaborator) >>> ddaux=read.maimages(files=targets.micro$FileName,source="agilent", >>> + >>> other.columns=list(IsGeneDetected="gIsGeneDetected", >>> + >>> IsSaturated >>> ="gIsSaturated", >>> + >>> IsFeatNonUnifOF >>> ="gIsFeatNonUnifOL", >>> + >>> IsFeatPopnOL >>> ="gIsFeatPopnOL", >>> + >>> BGKmd >>> ="gBGMedianSignal"), >>> + columns=list(Rf="gTotalGeneSignal", >>> + >>> Gf="gTotalProbeSignal", >>> + >>> Rb="gTotalGeneSignal", >>> + >>> Gb="gProcessedSignal"), >>> + verbose=TRUE,sep="\t",quote="") >>>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = T, >>> makePLOTpost = T, targets.micro, verbose = TRUE) >>> Error in density.default(object[, n], na.rm = TRUE) : >>> need at least 2 points to select a bandwidth automatically >>>> >>>> ddNORM = tgsNormalization(ddTGS, "quantile", makePLOTpre = F, >>> makePLOTpost = F, targets.micro, verbose = TRUE) >>> Error in xy.coords(x, y) : 'x' and 'y' lengths differ >>>> >>>> >>>> ddTGS.rma = rmaMicroRna(ddaux, normalize = TRUE, background = TRUE) >>> Error in split.default(0:(length(pNList) - 1), pNList) : >>> Group length is 0 but data length > 0 >>> # this takes quite a few minutes to process, then gives this error >>> >>> I've seen quite a bit of Agilent microRNA data through our centre, >>> and >>> can't recall ever seeing a chr_coord column, so is this to do with >>> different versions of Agilent Feature Extraction, or different >>> defaults set by the array facility? >>> >>> I'd really like to RMA normalize these data, so any help would be >>> really appreciated >>> >>> cheers, >>> Mark >>> >>> >>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> i386-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] AgiMicroRna_1.2.0 preprocessCore_1.10.0 affy_1.26.1 >>> limma_3.4.3 Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.16.0 tools_2.11.1 >>>> >>> >>> >>> ----------------------------------------------------- >>> Mark Cowley, PhD >>> >>> Peter Wills Bioinformatics Centre >>> Garvan Institute of Medical Research, Sydney, Australia >>> ----------------------------------------------------- >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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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