Dear Constanze,

RMA is appropriate for Affymetrix arrays and can be applied to Agilent
microRNA
arrays, eg. via package AgiMicroRna as you have tried, but apparently your
data
is from Agilent gene expression arrays where RMA and AgiMicroRna do not make
sense. I would recommend to use limma and follow the excellent user's guide
for
importing and preprocessing your data.

Cheers,

 - axel


On Sat, Feb 23, 2013 at 10:10 PM, Constanze [guest]
<guest@bioconductor.org>wrote:

>
> Dear All,
>
> i have Agilent gene expression data (SurePrint G3 Human Gene Expression
> 8x60K v2 Microarray; chip type G4858A-039494) data. Feature extraction was
> done setting  TextOutPkgType="Full". I want to rma-normalize this data but
> realize i'm missing two of the columns required by readMicroRnaAFE in
> AgiMicroRna : gTotalGeneSignal and gTotalProbeSignal.
>
> Here is the list of features i have on the chip:
> FEATURES        FeatureNum      Row     Col     accessions      chr_coord
> SubTypeMask     SubTypeName     Start   Sequence        ProbeUID
>  ControlType     ProbeName       GeneName        SystematicName
>  Description     PositionX       PositionY       gSurrogateUsed  gIsFound
>      gProcessedSignal        gProcessedSigError      gNumPixOLHi
> gNumPixOLLo     gNumPix gMeanSignal     gMedianSignal   gPixSDev
>  gPixNormIQR     gBGNumPix       gBGMeanSignal   gBGMedianSignal gBGPixSDev
>      gBGPixNormIQR   gNumSatPix      gIsSaturated    gIsFeatNonUnifOL
>  gIsBGNonUnifOL  gIsFeatPopnOL   gIsBGPopnOL     IsManualFlag
>  gBGSubSignal    gBGSubSigError  gIsPosAndSignif gPValFeatEqBG   gNumBGUsed
>      gIsWellAboveBG  gBGUsed gBGSDUsed       ErrorModel
>  gSpatialDetrendIsInFilteredSet  gSpatialDetrendSurfaceValue
> SpotExtentX     SpotExtentY     gNetSignal      gMultDetrendSignal
>  gProcessedBackground    gProcessedBkngError     IsUsedBGAdjust
>  gInterpolatedNegCtrlSub gIsInNegCtrlRange       gIsUsedInMD
>
>
> If AgiMicroRna is not adapted for this type of data, are there any good
> alternatives?
>
>
> Thanks very much,
>
> Constanze
>
>
>
>  -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=de_CH.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=de_CH.UTF-8        LC_COLLATE=de_CH.UTF-8
>  [5] LC_MONETARY=de_CH.UTF-8    LC_MESSAGES=de_DE.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] AgiMicroRna_2.6.0     affycoretools_1.28.0  KEGG.db_2.7.1
>  [4] GO.db_2.7.1           RSQLite_0.11.2        DBI_0.2-5
>  [7] AnnotationDbi_1.18.4  preprocessCore_1.18.0 affy_1.34.0
> [10] limma_3.12.3          Biobase_2.16.0        BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.24.0       annaffy_1.28.0      annotate_1.34.1
>  [4] BiocInstaller_1.4.9 biomaRt_2.12.0      Biostrings_2.24.1
>  [7] Category_2.22.0     gcrma_2.28.0        genefilter_1.38.0
> [10] GOstats_2.22.0      graph_1.34.0        grid_2.15.1
> [13] GSEABase_1.18.0     IRanges_1.14.4      lattice_0.20-10
> [16] RBGL_1.32.1         RCurl_1.95-3        splines_2.15.1
> [19] stats4_2.15.1       survival_2.36-14    tools_2.15.1
> [22] XML_3.95-0.1        xtable_1.7-0        zlibbioc_1.2.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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>



-- 


Axel Klenk
Research Informatician
Information Management Drug Discovery

Actelion Pharmaceuticals Ltd. • Gewerbestrasse 16 • CH-4123 Allschwil •
Switzerland
G12.O1.R10

axel.klenk@actelion.com • www.actelion.com
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