[BioC] Reading Agilent files using read.maimages
Scott Reagan Franklin
drscottfranklin at gmail.com
Wed Aug 15 15:58:45 CEST 2007
Steve:
It should be noted that when you are using read.maimages with
source="agilent" and you are using the actual Agilent Raw Data file,
you will, by default, have RG$R and RG$G equal to the rMeanSignal and
gMeanSignal. In order to specify that they be equal to the
rProcessedSignal and gProcessedSignal you need to add an option to
read.maimages:
RG<-read.maimages(targets$FileName,path=".",columns=list(R="rProcessedSignal",G="gProcessedSignal));
You can also specify which background signal is used as well by
including in Rb and Gb in the list above. By default Rb and Gb are
chosen as the median background signals.
--
Scott Franklin, Ph.D.
--------------------------------------------------
Bioinformaticist
Post-Doctoral Research Associate
Plant and Soil Science
Texas Tech University
--------------------------------------------------
Adjunct Professor of Mathematics
Wayland Baptist University
--------------------------------------------------
http://blog.drscottfranklin.net
Steve Taylor wrote:
> Hi,
>
> I am trying to read a set of Agilent (Human 1A Microarray(V2)[G4110B] (A-AGIL-9)) files from ArrayExpress, accession E-MEXP-668, using read.maimages. I haven't processed Agilent files before (or used
> read.maimages for that matter!) so sorry if this a basic question but I am wondering if there is a problem parsing the data or perhaps I am doing something wrong....
>
> I downloaded the raw data from ArrayExpress. I then read in the data like this:
>
> > RG<-read.maimages(targets$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
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