Question: FW: normalization one color microarrays
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gravatar for Paz Tapia Ramirez
7.7 years ago by
Paz Tapia Ramirez150 wrote:
Step 14 is: ################################################### ### chunk number 14: filter.probes ################################################### ddFILT=filter.probes(ddNORM, control=TRUE, wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE, sat=TRUE, PopnOL=TRUE, NonUnifOL=T, nas=TRUE, limWellAbove=75, limISF=75, limNEG=75, limSAT=75, limPopnOL=75, limNonUnifOL=75, limNAS=100, makePLOT=F,annotation.package="hgug4112a.db",flag.counts=T,targets) I can run the step 13 (Correction background and Normalization). sessionInfo() says: R version 2.11.1 (2010-05-31) i686-pc-linux-gnu locale: [1] LC_CTYPE=es_ES.utf8 LC_NUMERIC=C [3] LC_TIME=es_ES.utf8 LC_COLLATE=es_ES.utf8 [5] LC_MONETARY=C LC_MESSAGES=es_ES.utf8 [7] LC_PAPER=es_ES.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=es_ES.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] vsn_3.16.0 annotate_1.26.1 hgug4112a.db_2.4.1 [4] org.Hs.eg.db_2.4.1 RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.10.2 Biobase_2.8.0 marray_1.26.0 [10] limma_3.4.5 loaded via a namespace (and not attached): [1] affy_1.26.1 affyio_1.16.0 grid_2.11.1 [4] lattice_0.19-26 preprocessCore_1.10.0 xtable_1.5-6 and specifically in step 14 says: FILTERING BY ControlType FLAG ------------------------------------------------------ PROBES BEFORE FILTERING: 45220 PROBES AFTER ControlType FILTERING: 0 RAW DATA WITHOUT CONTROLS OUT : 0 ------------------------------------------------------ FILTERING BY IsWellAboveBG filterFLAG FLAG FILTERING OPTIONS - FLAG OK = 1 - limWellAbove: 75 % PROBES BEFORE FILTERING: 0 PROBES AFTER QC FILTERING: 0 IsNOTWellAboveBG OUT : 0 ------------------------------------------------------ FILTERING BY gIsFound filterFLAG FLAG FILTERING OPTIONS - FLAG OK = 1 - limISF: 75 % PROBES AFTER gIsFound FILTERING: 0 IsNOTFound OUT : 0 ------------------------------------------------------ Error en if (aux[jj] >= Limit[pos[jj]]) { : valor ausente donde TRUE/FALSE es necesario Thanks, Paz From: johannes.freudenberg@nih.gov To: verotapia at alumnos.utalca.cl CC: bioconductor at stat.math.ethz.ch Date: Mon, 29 Aug 2011 13:12:42 -0400 Subject: RE: [BioC] normalization one color microarrays Can you please be more specific? I?m not really sure what step 14 is. What exactly doesn?t work? Please provide an example that doesn?t work for you and the kind of error messages it produces. It?s also a good idea to provide the output of > sessionInfo() when you post a question like this to the list. --Johannes From: Paz Tapia Ramirez [mailto:verotapia at alumnos.utalca.cl] Sent: Monday, August 29, 2011 1:06 PM To: Freudenberg, Johannes (NIH/NIEHS) [E] Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] normalization one color microarrays when I work with Agi4x44PreProcess, from step 14 onwards it does not workFrom: johannes.freudenberg at nih.gov To: verotapia at alumnos.utalca.cl CC: bioconductor at stat.math.ethz.ch Date: Mon, 29 Aug 2011 13:01:46 -0400 Subject: RE: [BioC] normalization one color microarraysHi Paz, I?m not exactly sure what kind of microarrays you are trying to process but I?m guessing you are talking about Agilent 4x44 gene expression arrays. If that is the case, I would recommend to use the Agi4x44Preprocess package. You can download this package here: http: //www.bioconductor.org/packages/2.3/bioc/html/Agi4x44PreProcess.html or by running the following in R > source("http://bioconductor.org/biocLite.R")> biocLite("Agi4x44PreProcess") This package comes with a nice manual which explains all the steps. It also has plenty of examples you can try. You can find the manual here: http://www.bioconductor.org/packag es/2.3/bioc/vignettes/Agi4x44PreProcess/inst/doc/Agi4x44PreProcess.pdf I hope this helps for now. Let me know if you more specific questions. --Johannes From: Paz Tapia Ramirez [mailto:verotapia at alumnos.utalca.cl] Sent: Monday, August 29, 2011 12:25 PM To: Freudenberg, Johannes (NIH/NIEHS) [E]; bioconductor at stat.math.ethz.ch; bioconductor-bounces at r-project.org Subject: RE: [BioC] normalization one color microarrays Hi, but if I make not summarization process, how do I build the set of expression?> From: johannes.freudenberg at nih.gov > To: verotapia at alumnos.utalca.cl > Date: Wed, 24 Aug 2011 16:17:07 -0400 > Subject: RE: [BioC] normalization one color microarrays > > Summarization really only applies to Affymetrix arrays where you have several probes per probeset. > > --Johannes > > > -----Original Message----- > From: Paz Tapia Ramirez [mailto:verotapia at alumnos.utalca.cl] > Sent: Wednesday, August 24, 2011 4:09 PM > To: bioconductor at stat.math.ethz.ch; bioconductor-bounces at r-project.org > Subject: [BioC] normalization one color microarrays > > > > > > > > > > > Hello, I am starting to work with ONE color microarrays from Agilent, and I read that during the pre-processing is main tasks, such as background adjustment, normalization and summarization. Currently I have corrected the background and normalized samples, but do not understand the step of the summarization. Can you help me please? > > Thks, > Paz > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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