[BioC] how to use limma on this format

[smohapat at vbi.vt.edu]

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
>
>
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