AgiMicroRna for new Agilent Chip format - columns gTotalGeneSignal and gTotalProbeSignal missing
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Last seen 8.3 years ago
Dear All, i have Agilent gene expression data (SurePrint G3 Human Gene Expression 8x60K v2 Microarray; chip type G4858A-039494) data. Feature extraction was done setting TextOutPkgType="Full". I want to rma- normalize this data but realize i'm missing two of the columns required by readMicroRnaAFE in AgiMicroRna : gTotalGeneSignal and gTotalProbeSignal. Here is the list of features i have on the chip: FEATURES FeatureNum Row Col accessions chr_coord SubTypeMask SubTypeName Start Sequence ProbeUID ControlType ProbeName GeneName SystematicName Description PositionX PositionY gSurrogateUsed gIsFound gProcessedSignal gProcessedSigError gNumPixOLHi gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev gPixNormIQR gBGNumPix gBGMeanSignal gBGMedianSignal gBGPixSDev gBGPixNormIQR gNumSatPix gIsSaturated gIsFeatNonUnifOL gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag gBGSubSignal gBGSubSigError gIsPosAndSignif gPValFeatEqBG gNumBGUsed gIsWellAboveBG gBGUsed gBGSDUsed ErrorModel gSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue SpotExtentX SpotExtentY gNetSignal gMultDetrendSignal gProcessedBackground gProcessedBkngError IsUsedBGAdjust gInterpolatedNegCtrlSub gIsInNegCtrlRange gIsUsedInMD If AgiMicroRna is not adapted for this type of data, are there any good alternatives? Thanks very much, Constanze -- output of sessionInfo(): R version 2.15.1 (2012-06-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_CH.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_CH.UTF-8 LC_COLLATE=de_CH.UTF-8 [5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AgiMicroRna_2.6.0 affycoretools_1.28.0 KEGG.db_2.7.1 [4] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 [7] AnnotationDbi_1.18.4 preprocessCore_1.18.0 affy_1.34.0 [10] limma_3.12.3 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 [4] BiocInstaller_1.4.9 biomaRt_2.12.0 Biostrings_2.24.1 [7] Category_2.22.0 gcrma_2.28.0 genefilter_1.38.0 [10] GOstats_2.22.0 graph_1.34.0 grid_2.15.1 [13] GSEABase_1.18.0 IRanges_1.14.4 lattice_0.20-10 [16] RBGL_1.32.1 RCurl_1.95-3 splines_2.15.1 [19] stats4_2.15.1 survival_2.36-14 tools_2.15.1 [22] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
GO AgiMicroRna GO AgiMicroRna • 1.3k views
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Axel Klenk ▴ 990
@axel-klenk-3224
Last seen 20 hours ago
Switzerland
Dear Constanze, RMA is appropriate for Affymetrix arrays and can be applied to Agilent microRNA arrays, eg. via package AgiMicroRna as you have tried, but apparently your data is from Agilent gene expression arrays where RMA and AgiMicroRna do not make sense. I would recommend to use limma and follow the excellent user's guide for importing and preprocessing your data. Cheers, - axel On Sat, Feb 23, 2013 at 10:10 PM, Constanze [guest] <guest@bioconductor.org>wrote: > > Dear All, > > i have Agilent gene expression data (SurePrint G3 Human Gene Expression > 8x60K v2 Microarray; chip type G4858A-039494) data. Feature extraction was > done setting TextOutPkgType="Full". I want to rma-normalize this data but > realize i'm missing two of the columns required by readMicroRnaAFE in > AgiMicroRna : gTotalGeneSignal and gTotalProbeSignal. > > Here is the list of features i have on the chip: > FEATURES FeatureNum Row Col accessions chr_coord > SubTypeMask SubTypeName Start Sequence ProbeUID > ControlType ProbeName GeneName SystematicName > Description PositionX PositionY gSurrogateUsed gIsFound > gProcessedSignal gProcessedSigError gNumPixOLHi > gNumPixOLLo gNumPix gMeanSignal gMedianSignal gPixSDev > gPixNormIQR gBGNumPix gBGMeanSignal gBGMedianSignal gBGPixSDev > gBGPixNormIQR gNumSatPix gIsSaturated gIsFeatNonUnifOL > gIsBGNonUnifOL gIsFeatPopnOL gIsBGPopnOL IsManualFlag > gBGSubSignal gBGSubSigError gIsPosAndSignif gPValFeatEqBG gNumBGUsed > gIsWellAboveBG gBGUsed gBGSDUsed ErrorModel > gSpatialDetrendIsInFilteredSet gSpatialDetrendSurfaceValue > SpotExtentX SpotExtentY gNetSignal gMultDetrendSignal > gProcessedBackground gProcessedBkngError IsUsedBGAdjust > gInterpolatedNegCtrlSub gIsInNegCtrlRange gIsUsedInMD > > > If AgiMicroRna is not adapted for this type of data, are there any good > alternatives? > > > Thanks very much, > > Constanze > > > > -- output of sessionInfo(): > > R version 2.15.1 (2012-06-22) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_CH.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_CH.UTF-8 LC_COLLATE=de_CH.UTF-8 > [5] LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AgiMicroRna_2.6.0 affycoretools_1.28.0 KEGG.db_2.7.1 > [4] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 > [7] AnnotationDbi_1.18.4 preprocessCore_1.18.0 affy_1.34.0 > [10] limma_3.12.3 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 annaffy_1.28.0 annotate_1.34.1 > [4] BiocInstaller_1.4.9 biomaRt_2.12.0 Biostrings_2.24.1 > [7] Category_2.22.0 gcrma_2.28.0 genefilter_1.38.0 > [10] GOstats_2.22.0 graph_1.34.0 grid_2.15.1 > [13] GSEABase_1.18.0 IRanges_1.14.4 lattice_0.20-10 > [16] RBGL_1.32.1 RCurl_1.95-3 splines_2.15.1 > [19] stats4_2.15.1 survival_2.36-14 tools_2.15.1 > [22] XML_3.95-0.1 xtable_1.7-0 zlibbioc_1.2.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Axel Klenk Research Informatician Information Management Drug Discovery Actelion Pharmaceuticals Ltd. • Gewerbestrasse 16 • CH-4123 Allschwil • Switzerland G12.O1.R10 axel.klenk@actelion.com • www.actelion.com Address for visitors: Hegenheimermattweg 91 -- The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com [[alternative HTML version deleted]]
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