how to use limma on this format
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Weiwei Shi ★ 1.2k
@weiwei-shi-1407
Last seen 10.2 years ago
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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@saroj-mohapatra-1446
Last seen 10.2 years ago
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 > >
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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
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Weiwei Shi wrote: > 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. Hi, Weiwei. You will probably benefit from a quick read of the read.maimages help. <quote> columns: list with fields 'R', 'G', 'Rb' and 'Gb' giving the column names to be used for red and green foreground and background or, in the case of Imagene data, a list with fields 'f' and 'b'. This argument is optional if 'source' is specified, otherwise it is required. other.columns: character vector of names of other columns to be read containing spot-specific information annotation: character vector of names of columns containing annotation information about the probes </quote> So, you can specify any columns you like. Also, if there is a header to the file as in most Agilent files, you will want to pass skip=9 to read.maimages which, according to the help for read.maimages, will be passed along to read.table. I hope that clarifies things a bit. Sean
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Thanks. That should solve my problem. Sorry I did not read carefully before I posted. On 7/17/07, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > Weiwei Shi wrote: > > 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. > > Hi, Weiwei. You will probably benefit from a quick read of the > read.maimages help. > > <quote> > columns: list with fields 'R', 'G', 'Rb' and 'Gb' giving the column > names to be used for red and green foreground and background > or, in the case of Imagene data, a list with fields 'f' and > 'b'. This argument is optional if 'source' is specified, > otherwise it is required. > > other.columns: character vector of names of other columns to be read > containing spot-specific information > > annotation: character vector of names of columns containing annotation > information about the probes > </quote> > > So, you can specify any columns you like. Also, if there is a header to > the file as in most Agilent files, you will want to pass skip=9 to > read.maimages which, according to the help for read.maimages, will be > passed along to read.table. > > I hope that clarifies things a bit. > > Sean > -- 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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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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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 > > _______________________________________________ > 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
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Weiwei Shi wrote: > 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! > You will probably want to get the manual for the Agilent Feature Extraction software to review the definitions of the columns (available from Agilent or on the computer on which the slides were scanned). Agilent provides copious information for use in quality assessment. Generally speaking, though, you have two-color data and many of the principles are the same as for other two-color array systems. Sean
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