[BioC] Reading Agilent files using read.maimages

[Steve Taylor]

Hi,

I am trying to read a set of Agilent (Human 1A Microarray(V2)[G4110B] (A-AGIL-9)) files from ArrayExpress, accession E-MEXP-668, using read.maimages. I haven't processed Agilent files before (or used 
read.maimages for that matter!) so sorry if this a basic question but I am wondering if there is a problem parsing the data or perhaps I am doing something wrong....

I downloaded the raw data from ArrayExpress. I then read in the data like this:

 > RG<-read.maimages(targets$FileName,path=".",source="agilent");
Read ./E-MEXP-668-raw-data-921408043.txt
Read ./E-MEXP-668-raw-data-921408048.txt
Read ./E-MEXP-668-raw-data-921408053.txt
Read ./E-MEXP-668-raw-data-921408058.txt
Read ./E-MEXP-668-raw-data-921408063.txt
Read ./E-MEXP-668-raw-data-921408068.txt
Read ./E-MEXP-668-raw-data-921408073.txt
Read ./E-MEXP-668-raw-data-921408078.txt
Read ./E-MEXP-668-raw-data-921408083.txt
Read ./E-MEXP-668-raw-data-921408088.txt
Read ./E-MEXP-668-raw-data-921408093.txt
Read ./E-MEXP-668-raw-data-921408098.txt
Read ./E-MEXP-668-raw-data-921408103.txt
Read ./E-MEXP-668-raw-data-921408108.txt
Read ./E-MEXP-668-raw-data-921408113.txt
Read ./E-MEXP-668-raw-data-921408118.txt
Read ./E-MEXP-668-raw-data-921408123.txt
Read ./E-MEXP-668-raw-data-921408128.txt
Read ./E-MEXP-668-raw-data-921408133.txt
Read ./E-MEXP-668-raw-data-921408138.txt
Read ./E-MEXP-668-raw-data-921408143.txt

Querying the object...
 > names(RG)
[1] "G"       "Gb"      "R"       "Rb"      "targets" "source"

 > dim(RG)
[1]  0 21


 >RG$R
      E-MEXP-668-raw-data-921408043 E-MEXP-668-raw-data-921408048
      E-MEXP-668-raw-data-921408053 E-MEXP-668-raw-data-921408058
      E-MEXP-668-raw-data-921408063 E-MEXP-668-raw-data-921408068
      E-MEXP-668-raw-data-921408073 E-MEXP-668-raw-data-921408078
      E-MEXP-668-raw-data-921408083 E-MEXP-668-raw-data-921408088
      E-MEXP-668-raw-data-921408093 E-MEXP-668-raw-data-921408098
      E-MEXP-668-raw-data-921408103 E-MEXP-668-raw-data-921408108
      E-MEXP-668-raw-data-921408113 E-MEXP-668-raw-data-921408118
      E-MEXP-668-raw-data-921408123 E-MEXP-668-raw-data-921408128
      E-MEXP-668-raw-data-921408133 E-MEXP-668-raw-data-921408138
      E-MEXP-668-raw-data-921408143

 > RG$G
      E-MEXP-668-raw-data-921408043 E-MEXP-668-raw-data-921408048
      E-MEXP-668-raw-data-921408053 E-MEXP-668-raw-data-921408058
      E-MEXP-668-raw-data-921408063 E-MEXP-668-raw-data-921408068
      E-MEXP-668-raw-data-921408073 E-MEXP-668-raw-data-921408078
      E-MEXP-668-raw-data-921408083 E-MEXP-668-raw-data-921408088
      E-MEXP-668-raw-data-921408093 E-MEXP-668-raw-data-921408098
      E-MEXP-668-raw-data-921408103 E-MEXP-668-raw-data-921408108
      E-MEXP-668-raw-data-921408113 E-MEXP-668-raw-data-921408118
      E-MEXP-668-raw-data-921408123 E-MEXP-668-raw-data-921408128
      E-MEXP-668-raw-data-921408133 E-MEXP-668-raw-data-921408138
      E-MEXP-668-raw-data-921408143


A typical header for one of these raw files is

CompositeSequence Identifier    Database ebi.ac.uk:Database:embl        Database ebi.ac.uk:Database:ensembl     Database ebi.ac.uk:Database:locus       Database ebi.ac.uk:Database:refseq      Database 
ebi.ac.uk:Database:tigr_thc    Database www.chem.agilent.com:Database:agc      Database www.chem.agilent.com:Database:agp      Feature coordinates: metaColumn metaRow column  row     Reporter control 
type   Reporter group  Reporter identifier     Reporter name   Reporter sequence type  H_C1 A_mock A and B/FEATURES    H_C1 A_mock A and B/FeatureNum  H_C1 A_mock A and B/gbpri       H_C1 A_mock A and 
B/gp  H_C1 A_mock A and B/sp  H_C1 A_mock A and B/ProbeUID    H_C1 A_mock A and B/ControlType H_C1 A_mock A and B/ProbeName   H_C1 A_mock A and B/GeneName    H_C1 A_mock A and B/SystematicName 
H_C1 A_mock A and B/Description H_C1 A_mock A and B/LogRatio    H_C1 A_mock A and B/LogRatioError       H_C1 A_mock A and B/PValueLogRatio      H_C1 A_mock A and B/gSurrogateUsed      H_C1 A_mock A 
and B/rSurrogateUsed      H_C1 A_mock A and B/gIsFound    H_C1 A_mock A and B/rIsFound    H_C1 A_mock A and B/gProcessedSignal    H_C1 A_mock A and B/rProcessedSignal    H_C1 A_mock A and 
B/gProcessedSigError  H_C1 A_mock A and B/rProcessedSigError  H_C1 A_mock A and B/gNumPixOLHi H_C1 A_mock A and B/rNumPixOLHi H_C1 A_mock A and B/gNumPixOLLo H_C1 A_mock A and B/rNumPixOLLo H_C1 
A_mock A and B/gNumPix     H_C1 A_mock A and B/rNumPix     H_C1 A_mock A and B/gMeanSignal H_C1 A_mock A and B/rMeanSignal H_C1 A_mock A and B/gMedianSignal       H_C1 A_mock A and B/rMedianSignal 
    H_C1 A_mock A and B/gPixSDev    H_C1 A_mock A and B/rPixSDev    H_C1 A_mock A and B/gBGNumPix   H_C1 A_mock A and B/rBGNumPix   H_C1 A_mock A and B/gBGMeanSignal       H_C1 A_mock A and 
B/rBGMeanSignal       H_C1 A_mock A and B/gBGMedianSignal     H_C1 A_mock A and B/rBGMedianSignal     H_C1 A_mock A and B/gBGPixSDev  H_C1 A_mock A and B/rBGPixSDev  H_C1 A_mock A and B/gNumSatPix 
H_C1 A_mock A and B/rNumSatPix  H_C1 A_mock A and B/gIsSaturated        H_C1 A_mock A and B/rIsSaturated        H_C1 A_mock A and B/PixCorrelation      H_C1 A_mock A and B/BGPixCorrelation    H_C1 
A_mock A and B/gIsFeatNonUnifOL    H_C1 A_mock A and B/rIsFeatNonUnifOL    H_C1 A_mock A and B/gIsBGNonUnifOL      H_C1 A_mock A and B/rIsBGNonUnifOL      H_C1 A_mock A and B/gIsFeatPopnOL       H_C1 
A_mock A and B/rIsFeatPopnOL       H_C1 A_mock A and B/gIsBGPopnOL H_C1 A_mock A and B/rIsBGPopnOL H_C1 A_mock A and B/IsManualFlag        H_C1 A_mock A and B/gBGSubSignal        H_C1 A_mock A and 
B/rBGSubSignal        H_C1 A_mock A and B/gBGSubSigError      H_C1 A_mock A and B/rBGSubSigError      H_C1 A_mock A and B/BGSubSigCorrelation H_C1 A_mock A and B/gIsPosAndSignif     H_C1 A_mock A and 
B/rIsPosAndSignif     H_C1 A_mock A and B/gPValFeatEqBG       H_C1 A_mock A and B/rPValFeatEqBG       H_C1 A_mock A and B/gNumBGUsed  H_C1 A_mock A and B/rNumBGUsed  H_C1 A_mock A and B/gIsWellAboveBG 
      H_C1 A_mock A and B/rIsWellAboveBG      H_C1 A_mock A and B/IsUsedBGAdjust      H_C1 A_mock A and B/gBGUsed     H_C1 A_mock A and B/rBGUsed     H_C1 A_mock A and B/gBGSDUsed   H_C1 A_mock A and 
B/rBGSDUsed   H_C1 A_mock A and B/IsNormalization     H_C1 A_mock A and B/gDyeNormSignal      H_C1 A_mock A and B/rDyeNormSignal      H_C1 A_mock A and B/gDyeNormError       H_C1 A_mock A and 
B/rDyeNormError       H_C1 A_mock A and B/DyeNormCorrelation  H_C1 A_mock A and B/ErrorModel

Does this look correct? How do I get access to the intensities, for example to do a boxplot?

Thanks in advance for any help,

Steve


 > sessionInfo()
R version 2.5.1 (2007-06-27)
sparc-sun-solaris2.9

locale:
C

attached base packages:
  [1] "tcltk"     "splines"   "tools"     "stats"     "graphics"  "grDevices"
  [7] "utils"     "datasets"  "methods"   "base"

other attached packages:
     convert      marray   tkWidgets      DynDoc widgetTools  arrayMagic
    "1.10.0"    "1.14.0"    "1.14.0"    "1.14.0"    "1.12.0"    "1.14.0"
  genefilter    survival         vsn        affy      affyio       limma
    "1.14.1"      "2.32"     "2.2.0"    "1.14.2"     "1.4.1"    "2.10.5"
     Biobase
    "1.14.1"