[BioC] Reading Agilent files using read.maimages

[Sean Davis]

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

This is not an Agilent Raw Data file, I do not think.  The column names
are similar, but ArrayExpress has significantly changed the file from
its original format.  That said, the columns with "LogRatio",
"rProcessedSignal" and "gProcessedSignal" are the columns of interest
that have already been background corrected and, typically, a
normalization method applied (not sure which one without some more
description of the scanner settings).

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

I'm not sure if the files loaded correctly, given my comments above.
RG$R and RG$G contain the Red and Green intensities, if it loaded correctly.

Sean