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]]

