Question

cvArray error from AgiMicroRna package

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Daniel Brewer ★ 1.9k

@daniel-brewer-1791

Last seen 9.6 years ago

Hello, I am trying to analyse a series of Agilent microRNA arrays using the AgiMicroRna package. When I run the cvArray function I get the following error: Error in cvArray(dd.micro, "MeanSignal", targets.micro, verbose = TRUE) : NOT DUPLICATED ProbeName in chip Any ideas what this means and how to fix it? Interetsing dd.micro$genes does not have a column called ProbeName or GeneName like it suggests in the Vignette, but it does have ProbeUID. This is a bit odd as the datafiles do have a column called ProbeName and GeneName. The steps I have taken before this are as follows: > library("AgiMicroRna") > targets.micro <- readTargets(infile="Input/Targets.csv",verbose=TRUE) #TotalProbeSignal > td <- getwd() > setwd("Input/FE files") > dd.micro <- readMicroRnaAFE(targets.micro,verbose=TRUE) > setwd(td) Many thanks Dan P.S, > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_1.0.0 preprocessCore_1.8.0 affy_1.24.0 [4] limma_3.2.1 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 tools_2.10.1 -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

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ADD COMMENT • link 14.2 years ago Daniel Brewer ★ 1.9k

score 0 · Answer 1 · 2010-02-12

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Daniel Brewer ★ 1.9k

@daniel-brewer-1791

Last seen 9.6 years ago

On 11/02/2010 4:18 PM, Daniel Brewer wrote: > Hello, > > I am trying to analyse a series of Agilent microRNA arrays using the > AgiMicroRna package. When I run the cvArray function I get the > following error: > Error in cvArray(dd.micro, "MeanSignal", targets.micro, verbose = TRUE) : > NOT DUPLICATED ProbeName in chip > > Any ideas what this means and how to fix it? > > Interetsing dd.micro$genes does not have a column called ProbeName or > GeneName like it suggests in the Vignette, but it does have ProbeUID. > This is a bit odd as the datafiles do have a column called ProbeName and > GeneName. > > The steps I have taken before this are as follows: >> library("AgiMicroRna") >> targets.micro <- readTargets(infile="Input/Targets.csv",verbose=TRUE) > #TotalProbeSignal >> td <- getwd() >> setwd("Input/FE files") >> dd.micro <- readMicroRnaAFE(targets.micro,verbose=TRUE) >> setwd(td) > > Many thanks > > Dan I fixed this by allowing more columns form the genes column to be retained by readMicroRnaAFE. Dan The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

ADD COMMENT • link 14.2 years ago Daniel Brewer ★ 1.9k

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Hi, the cvArray function uses "which(duplicated(ddDUP$genes$ProbeName)==TRUE)" to get the duplicated Probes. If instead of having "ProbeName" you have "ProbeUID" the function is not going to work. The readMicroRnaAFE() uses read.maimages() from limma, and then we select what columns are retained in dd.micro. If we use read.maimages() directly, we´ll obtain: ddaux=read.maimages(files=targets$FileName,source="agilent", other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", ChrCoord="chr_coord", BGKmd="gBGMedianSignal", BGKus="gBGUsed"), columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMeanSignal", Gb="gProcessedSignal"), verbose=TRUE,sep="\t",quote="") > names(ddaux$genes) [1] "Row" "Col" "ProbeUID" "ControlType" [5] "ProbeName" "GeneName" "SystematicName" "Description" AFTER this, in readMicroRnaAFE() we subset the $genes: dd$genes=ddaux$genes[,c(4,5,6)], to retain: "ControlType", "ProbeName", and "GeneName". If you have "ProbeUID" in your RGList, some columns might be missing and the assignation in dd$genes=ddaux$genes[,c(4,5,6)] does not get the "ControlType", "ProbeName", and "GeneName". Try to use the "read.maimages" as i did above and you will have all the columns that you need. HTH p.- On Fri, Feb 12, 2010 at 2:50 PM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > On 11/02/2010 4:18 PM, Daniel Brewer wrote: > > Hello, > > > > I am trying to analyse a series of Agilent microRNA arrays using the > > AgiMicroRna package. When I run the cvArray function I get the > > following error: > > Error in cvArray(dd.micro, "MeanSignal", targets.micro, verbose = TRUE) : > > NOT DUPLICATED ProbeName in chip > > > > Any ideas what this means and how to fix it? > > > > Interetsing dd.micro$genes does not have a column called ProbeName or > > GeneName like it suggests in the Vignette, but it does have ProbeUID. > > This is a bit odd as the datafiles do have a column called ProbeName and > > GeneName. > > > > The steps I have taken before this are as follows: > >> library("AgiMicroRna") > >> targets.micro <- readTargets(infile="Input/Targets.csv",verbose=TRUE) > > #TotalProbeSignal > >> td <- getwd() > >> setwd("Input/FE files") > >> dd.micro <- readMicroRnaAFE(targets.micro,verbose=TRUE) > >> setwd(td) > > > > Many thanks > > > > Dan > > I fixed this by allowing more columns form the genes column to be > retained by readMicroRnaAFE. > > Dan > > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. 534147 > with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the...{{dropped:13}}

ADD REPLY • link 14.2 years ago Pedro Lopez-Romero ▴ 120