Question: Trouble using Agi4x44tPreProcess to anaylise old files
0
gravatar for matthew vitalone
7.5 years ago by
matthew vitalone30 wrote:
HI Bioconductor family, I am trying to analyise some old Agilent arrays which use version 7.5 for feature extraction using the latest Agi4x44PreProcess package. To make matters somewhat complicated, these are a mixture of 4x44 and older single slide arrays. First question is, can these be analyised together?? I have followed the notes and manual on that were provided with package to analyise these arrays. I am able to load the arrays, but I get the following error message: INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) : the script will stop now I have looked into the BioC archives, and have found that the only related advice is to change the column header names. Tried this but it did not work. Also, I have tried to use a modified fix posted by from Pedro for the miRNA questions about this, but that does not work either. Details of the aforementioned function: read.AgilentFE <- function(targets){ if (!is(targets, "data.frame")){ stop("'targets' must be a data.frame") } ddaux=read.maimages(files=targets$FileName,source="agilent", other.columns=list(IsGeneDetected="gIsGeneDetected", IsSaturated="gIsSaturated", IsFeatNonUnifOF="gIsFeatNonUnifOL", IsFeatPopnOL="gIsFeatPopnOL", BGKmd="gBGMedianSignal", BGKus="gBGUsed"), columns=list(Rf="gTotalGeneSignal", Gf="gTotalProbeSignal", Rb="gMeanSignal", Gb="gProcessedSignal"), verbose=T,sep="\t",quote="") dd=new("RGList") dd$R=ddaux$R dd$G=ddaux$G dd$Rb=ddaux$Rb dd$Gb=ddaux$Gb dd$targets=ddaux$targets dd$genes=ddaux$genes[,c(4,5,6)] dd$other=ddaux$other rm(ddaux) cat("","\n") cat(" RGList:","\n") cat(" dd$R: 'gTotalGeneSignal' ","\n") cat(" dd$G: 'gTotalProbeSignal' ","\n") cat(" dd$Rb: 'gMeanSignal' ","\n") cat(" dd$Gb: 'gProcessedSignal' ","\n") cat("","\n") return(dd) } As one can see, I am not a programer but a biological scientist trying to teach myself R. I am stuck and have no idea what to do. Is there a way to ignore these columns, as I don't need them. All that I am after is to do a simple differential expression analysis using limma. Any help would be much appreciated!!! I do apologise for the length of this email. I am using R2.14.1 in R stuido, with all bioconductor packages updated in the past 48hrs Thanks, Matthew Here is the details of the R session: > setwd("G:/Desktop PC/HD/Matthew/Projects/TOL study/Agilent arrays")> library("hgug4112a.db")Loading required package: AnnotationDbiLoading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: org.Hs.eg.dbLoading required package: DBIWarning message:package ‘AnnotationDbi’ was built under R version 2.14.2 > library("Agi4x44PreProcess")Loading required package: limmaLoading required package: annotateLoading required package: genefilterWarning messages:1: package ‘limma’ was built under R version 2.14.2 2: package ‘annotate’ was built under R version 2.14.2 > targets=read.targets(infile="targets.txt") Target File FileName US14702375_251239126265_S01_A01_tol3 US14702375_251239126265_S01_A01_tol3.txt US14702375_251239126266_S01_A01_tol4 US14702375_251239126266_S01_A01_tol4.txt US14702375_251239126267_S01_A01_tol5 US14702375_251239126267_S01_A01_tol5.txt US14702375_251239126263_S01_A01 US14702375_251239126263_S01_A01.txt US14702375_251239112455_S02_A01 US14702375_251239112455_S02_A01.txt US14702375_251239121312_S01_A01 US14702375_251239121312_S01_A01.txt US45102891_251485012766_S01_GE2-v5_95_Feb07_1_1 (B295)_tol15 US45102891_251485012766_S01_GE2-v5_95_Feb07_1_1 (B295)_tol15.txt US45102891_251485012766_S01_GE2-v5_95_Feb07_1_2 (B312-1)_tol16 US45102891_251485012766_S01_GE2-v5_95_Feb07_1_2 (B312-1)_tol16.txt US14702375_251239126275_S01_A01 US14702375_251239126275_S01_A01.txt US14702375_251239126276_S01_A01 US14702375_251239126276_S01_A01.txt US14702375_251239126264_S01_A01 US14702375_251239126264_S01_A01.txt US14702375_251239121504_S02_A01 US14702375_251239121504_S02_A01.txt US14702375_251239121683_S02_A01 US14702375_251239121683_S02_A01.txt US14702375_251239131569_S01_A01 US14702375_251239131569_S01_A01.txt US14702375_251239131570_S01_A01 US14702375_251239131570_S01_A01.txt US14702375_251239131571_S01_A01 US14702375_251239131571_S01_A01.txt US14702375_251239131572_S01_A01 US14702375_251239131572_S01_A01.txt US14702375_251239131573_S01_A01 US14702375_251239131573_S01_A01.txt US14702375_251239121684_S01_A01 US14702375_251239121684_S01_A01.txt US14702375_251239121685_S01_A01 US14702375_251239121685_S01_A01.txt US14702375_251239121686_S01_A01 US14702375_251239121686_S01_A01.txt US14702375_251239126273_S01_A01 US14702375_251239126273_S01_A01.txt US14702375_251239125911_S02_A01 US14702375_251239125911_S02_A01.txt US45102891_251485014089_S01_GE2-v5_95_Feb07_1_1(B082)_can1 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_1(B082)_can1.txt US45102891_251485014089_S01_GE2-v5_95_Feb07_1_2(B175)_can2 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_2(B175)_can2.txt US45102891_251485014089_S01_GE2-v5_95_Feb07_1_3(B219)_can3 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_3(B219)_can3.txt US45102891_251485014089_S01_GE2-v5_95_Feb07_1_4(B239)_can9 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_4(B239)_can9.txt US45102891_251485014090_S01_GE2-v5_95_Feb07_1_1(B273)_can6 US45102891_251485014090_S01_GE2-v5_95_Feb07_1_1(B273)_can6.txt US45102891_251485027831_S01_GE2-v5_95_Feb07_1_1 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_1.txt US45102891_251485027831_S01_GE2-v5_95_Feb07_1_2 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_2.txt US45102891_251485027831_S01_GE2-v5_95_Feb07_1_3 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_3.txt US45102891_251485027831_S01_GE2-v5_95_Feb07_1_4 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_4.txt US14702375_251239126261_S02_A01 US14702375_251239126261_S02_A01.txt US14702375_251239126262_S01_A01 US14702375_251239126262_S01_A01.txt US14702375_251239126268_S01_A01 US14702375_251239126268_S01_A01.txt US14702375_251239126269_S01_A01 US14702375_251239126269_S01_A01.txt Treatment GErep US14702375_251239126265_S01_A01_tol3 TOL 2 US14702375_251239126266_S01_A01_tol4 TOL 2 US14702375_251239126267_S01_A01_tol5 TOL 2 US14702375_251239126263_S01_A01 TOL 2 US14702375_251239112455_S02_A01 TOL 2 US14702375_251239121312_S01_A01 TOL 2 US45102891_251485012766_S01_GE2-v5_95_Feb07_1_1 (B295)_tol15 TOL 2 US45102891_251485012766_S01_GE2-v5_95_Feb07_1_2 (B312-1)_tol16 TOL 2 US14702375_251239126275_S01_A01 AR 4 US14702375_251239126276_S01_A01 AR 4 US14702375_251239126264_S01_A01 AR 4 US14702375_251239121504_S02_A01 AR 4 US14702375_251239121683_S02_A01 AR 4 US14702375_251239131569_S01_A01 AR 4 US14702375_251239131570_S01_A01 AR 4 US14702375_251239131571_S01_A01 AR 4 US14702375_251239131572_S01_A01 AR 4 US14702375_251239131573_S01_A01 AR 4 US14702375_251239121684_S01_A01 CAN 5 US14702375_251239121685_S01_A01 CAN 5 US14702375_251239121686_S01_A01 CAN 5 US14702375_251239126273_S01_A01 CAN 5 US14702375_251239125911_S02_A01 CAN 5 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_1(B082)_can1 CAN 5 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_2(B175)_can2 CAN 5 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_3(B219)_can3 CAN 5 US45102891_251485014089_S01_GE2-v5_95_Feb07_1_4(B239)_can9 CAN 5 US45102891_251485014090_S01_GE2-v5_95_Feb07_1_1(B273)_can6 CAN 5 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_1 CAN 5 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_2 CAN 5 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_3 CAN 5 US45102891_251485027831_S01_GE2-v5_95_Feb07_1_4 CAN 5 US14702375_251239126261_S02_A01 STA 3 US14702375_251239126262_S01_A01 STA 3 US14702375_251239126268_S01_A01 HNC 1 US14702375_251239126269_S01_A01 HNC 1 > dd=read.AgilentFE(targets, makePLOT=FALSE)Read US14702375_251239126265_S01_A01_tol3.txt Read US14702375_251239126266_S01_A01_tol4.txt Read US14702375_251239126267_S01_A01_tol5.txt Read US14702375_251239126263_S01_A01.txt Read US14702375_251239112455_S02_A01.txt Read US14702375_251239121312_S01_A01.txt Read US45102891_251485012766_S01_GE2-v5_95_Feb07_1_1 (B295)_tol15.txt Read US45102891_251485012766_S01_GE2-v5_95_Feb07_1_2 (B312-1)_tol16.txt Read US14702375_251239126275_S01_A01.txt Read US14702375_251239126276_S01_A01.txt Read US14702375_251239126264_S01_A01.txt Read US14702375_251239121504_S02_A01.txt Read US14702375_251239121683_S02_A01.txt Read US14702375_251239131569_S01_A01.txt Read US14702375_251239131570_S01_A01.txt Read US14702375_251239131571_S01_A01.txt Read US14702375_251239131572_S01_A01.txt Read US14702375_251239131573_S01_A01.txt Read US14702375_251239121684_S01_A01.txt Read US14702375_251239121685_S01_A01.txt Read US14702375_251239121686_S01_A01.txt Read US14702375_251239126273_S01_A01.txt Read US14702375_251239125911_S02_A01.txt Read US45102891_251485014089_S01_GE2-v5_95_Feb07_1_1(B082)_can1.txt Read US45102891_251485014089_S01_GE2-v5_95_Feb07_1_2(B175)_can2.txt Read US45102891_251485014089_S01_GE2-v5_95_Feb07_1_3(B219)_can3.txt Read US45102891_251485014089_S01_GE2-v5_95_Feb07_1_4(B239)_can9.txt Read US45102891_251485014090_S01_GE2-v5_95_Feb07_1_1(B273)_can6.txt Read US45102891_251485027831_S01_GE2-v5_95_Feb07_1_1.txt Read US45102891_251485027831_S01_GE2-v5_95_Feb07_1_2.txt Read US45102891_251485027831_S01_GE2-v5_95_Feb07_1_3.txt Read US45102891_251485027831_S01_GE2-v5_95_Feb07_1_4.txt Read US14702375_251239126261_S02_A01.txt Read US14702375_251239126262_S01_A01.txt Read US14702375_251239126268_S01_A01.txt Read US14702375_251239126269_S01_A01.txt INPUT DATA DOES NOT CONTAIN - Sequence and chr_coord SCANN THE DATA USING AFE 9.5.3.1 Error in read.AgilentFE(targets, makePLOT = FALSE) : the script will stop now [[alternative HTML version deleted]]
mirna limma agi4x44preprocess • 535 views
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