[BioC] how to use limma on this format
Weiwei Shi
helprhelp at gmail.com
Tue Jul 17 18:53:21 CEST 2007
Hi,
I tried "agilent" and it works!!! The situation is like this: the data
provider does not give me any hint about the "source" and I did not
try.
A further question here is, if I want to continue with Quality
Assessment procedures, is there any online materials I can following
by using limma? (is limma's User's guide good for that purpose).
I knew there is a spot quality weight function and I am wondering
which column servers that purpose.
I am quite newbie for QC for Agilent data. Thanks for any suggestions!
Best,
Weiwei
On 7/17/07, J.delasHeras at ed.ac.uk <J.delasHeras at ed.ac.uk> wrote:
>
> 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
> Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
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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
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