[BioC] how to use limma on this format

[Weiwei Shi]

Hi there

thanks Saroj for the reply.

But I think I did not clearify my question: I knew it needs a
source=?, while in my case, it seems the format does not match any of
the available. So I am asking if I need to create by myself the output
from this read.maimages, i.e. RGList or if there is another way. I
don't know what format this data belongs to.

Best,

Weiwei



On 7/17/07, smohapat at vbi.vt.edu <smohapat at vbi.vt.edu> wrote:
> Hello Weiwei:
>
> Limma function read.maimages reads agilent data files.
>
> > ?read.maimages
>
> ---------
>
> Description
> Reads an RGList from a series of two-color microarray image analysis
> output files
>
> ...
>
> Arguments
> source: character string specifying the image analysis program which
> produced the output files. Choices are "generic", "agilent",
> "arrayvision", "bluefuse", "genepix", "genepix.custom", "genepix.median",
> "imagene", "quantarray", "scanarrayexpress", "smd.old", "smd", "spot" or
> "spot.close.open".
>
> ...
>
> ---------
>
> By default it reads the following columns for agilent.
> G = "gMeanSignal",
> Gb = "gBGMedianSignal",
> R = "rMeanSignal",
> Rb = "rBGMedianSignal")
>
> Best wishes,
>
> Saroj
>
>
>
> On Mon, July 16, 2007 7:45 pm, Weiwei Shi wrote:
> > Hi, there:
> >
> >
> > I have an agilent data format with colnames which look like the
> > followings. I am wondering how to proceed with this data by using limma to
> > do the QC. I mean, I probably can create some corresponding objects of
> > limma manually (like RGList from gMedianSignal...) but it is painful.
> > Anyone knows about this source or any suggestions to move
> > from there.
> >
> > Another question, can I find "locuslink id" for ProbeName for agilent?
> >
> >
> > thanks,
> >
> > the data columns are
> >> as.character(t0[9,])
> > [1] "FEATURES"                       "FeatureNum"
> > "Row"
> > [4] "Col"                            "Start"
> > "Sequence"
> > [7] "ProbeUID"                       "ControlType"
> > "ProbeName"
> > [10] "GeneName"                       "PositionX"
> > "PositionY"
> > [13] "LogRatio"                       "LogRatioError"
> > "PValueLogRatio"
> > [16] "gSurrogateUsed"                 "rSurrogateUsed"
> > "gIsFound"
> > [19] "rIsFound"                       "gProcessedSignal"
> > "rProcessedSignal"
> > [22] "gProcessedSigError"             "rProcessedSigError"
> > "gNumPixOLHi"
> > [25] "rNumPixOLHi"                    "gNumPixOLLo"
> > "rNumPixOLLo"
> > [28] "gNumPix"                        "rNumPix"
> > "gMeanSignal"
> > [31] "rMeanSignal"                    "gMedianSignal"
> > "rMedianSignal"
> > [34] "gPixSDev"                       "rPixSDev"
> > "gBGNumPix"
> > [37] "rBGNumPix"                      "gBGMeanSignal"
> > "rBGMeanSignal"
> > [40] "gBGMedianSignal"                "rBGMedianSignal"
> > "gBGPixSDev"
> > [43] "rBGPixSDev"                     "gNumSatPix"
> > "rNumSatPix"
> > [46] "gIsSaturated"                   "rIsSaturated"
> > "PixCorrelation"
> > [49] "BGPixCorrelation"               "gIsFeatNonUnifOL"
> > "rIsFeatNonUnifOL"
> > [52] "gIsBGNonUnifOL"                 "rIsBGNonUnifOL"
> > "gIsFeatPopnOL"
> > [55] "rIsFeatPopnOL"                  "gIsBGPopnOL"
> > "rIsBGPopnOL"
> > [58] "IsManualFlag"                   "gBGSubSignal"
> > "rBGSubSignal"
> > [61] "gBGSubSigError"                 "rBGSubSigError"
> > "BGSubSigCorrelation"
> > [64] "gIsPosAndSignif"                "rIsPosAndSignif"
> > "gPValFeatEqBG"
> > [67] "rPValFeatEqBG"                  "gNumBGUsed"
> > "rNumBGUsed"
> > [70] "gIsWellAboveBG"                 "rIsWellAboveBG"
> > "gBGUsed"
> > [73] "rBGUsed"                        "gBGSDUsed"
> > "rBGSDUsed"
> > [76] "IsNormalization"                "gDyeNormSignal"
> > "rDyeNormSignal"
> > [79] "gDyeNormError"                  "rDyeNormError"
> > "DyeNormCorrelation"
> > [82] "ErrorModel"                     "xDev"
> > "gSpatialDetrendIsInFilteredSet"
> > [85] "rSpatialDetrendIsInFilteredSet" "gSpatialDetrendSurfaceValue"
> > "rSpatialDetrendSurfaceValue"
> > [88] ""                               ""
> > ""
> >
> >
> >
> >
> > --
> > Weiwei Shi, Ph.D
> > Research Scientist
> > GeneGO, Inc.
> >
> >
> > "Did you always know?"
> > "No, I did not. But I believed..."
> > ---Matrix III
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
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> >
> >
>
>
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III