[BioC] Agilent Chip G4858A-039494: columns gTotalGeneSignal, gTotalProbeSignal missing for AgiMicroRna

[Constanze [guest]]

Dear All,

i recently got some Agilent (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


I'd appreciate any suggestions on how to treat this data set.

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     


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