[BioC] how to use limma on this format

[J.delasHeras at ed.ac.uk]

You tried source="agilent" and it didn't work?

You can always load any format with source="generic" and then  
specifying the columns that contain the red/green signal and  
background... but "agilent" is one of the options for 'source' and its  
defaults match column names in your data... so just to be clear, you  
already tried that and it didn't work? If it didn't, what error did  
you get?

Jose


Quoting Weiwei Shi <helprhelp at gmail.com>:

> 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:
>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>>
>>
>>
>
>
> --
> 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:   
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
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