Affy output
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@sarmah-chintanu-kumar-3440
Last seen 10.2 years ago
Hi All, I am having some trouble to do the annotation of the normalized genes for a set of Affymetrix file (cdf = HG-U133_Plus_2) using UniGene ID and then, creating the output table. I was mainly referring to the book, "Bioinformatics & Computational Biology Solutions Using R and Bioinformatics" but at one stage, I was unsure as to how to proceed. Any suggestion would be appreciated. Also, wonder if there is any other (quicker!) way of doing it ! Thank you ! Cheers, Chintanu > myRMA <- justRMA() > probeids4log2 <- featureNames (myRMA) > symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") > anncols <- aaf.handler ()[c(1,2,7,9)] > anntable4log2 <- aafTableAnn (probeids4log2, "hgu133plus2.db", anncols) > exprtable4log2 <- aafTableInt (myRMA, probeids=probeids4log2) > table4log2 <- merge (anntable4log2, exprtable4log2) > UniGeneID4log2 <- table4log2$UniGene # genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) > sessionInfo () R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0 siggenes_1.18.0 annaffy_1.16.0 KEGG.db_2.2.11 [7] GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.0 multtest_2.0.0 affy_1.22.0 [13] Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 MASS_7.2-46 preprocessCore_1.6.0 survival_2.35-4 tools_2.9.0 [[alternative HTML version deleted]]
Annotation GO hgu133a2 hgu133plus2 cdf Annotation GO hgu133a2 hgu133plus2 cdf • 1.2k views
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@james-w-macdonald-5106
Last seen 16 hours ago
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Hi Chintanu, Sarmah, Chintanu Kumar wrote: > Hi All, > > I am having some trouble to do the annotation of the normalized genes > for a set of Affymetrix file (cdf = HG-U133_Plus_2) using UniGene ID > and then, creating the output table. > > I was mainly referring to the book, "Bioinformatics & Computational > Biology Solutions Using R and Bioinformatics" but at one stage, I was > unsure as to how to proceed. > > Any suggestion would be appreciated. Also, wonder if there is any > other (quicker!) way of doing it ! I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs? Anyway, there are easier ways to do this. One such way is using probes2table() in affycoretools. probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") Best, Jim > > Thank you ! > > Cheers, > > Chintanu > > > >> myRMA <- justRMA() probeids4log2 <- featureNames (myRMA) >> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") anncols >> <- aaf.handler ()[c(1,2,7,9)] anntable4log2 <- aafTableAnn >> (probeids4log2, "hgu133plus2.db", anncols) exprtable4log2 <- >> aafTableInt (myRMA, probeids=probeids4log2) table4log2 <- merge >> (anntable4log2, exprtable4log2) UniGeneID4log2 <- >> table4log2$UniGene > # genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, > Log2=table4log2) >> sessionInfo () > R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base > packages: [1] splines stats graphics grDevices utils > datasets methods base other attached packages: [1] > hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0 > siggenes_1.18.0 annaffy_1.16.0 KEGG.db_2.2.11 [7] > GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > AnnotationDbi_1.6.0 multtest_2.0.0 affy_1.22.0 [13] > Biobase_2.4.1 loaded via a namespace (and not attached): [1] > affyio_1.12.0 MASS_7.2-46 preprocessCore_1.6.0 > survival_2.35-4 tools_2.9.0 > > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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@sarmah-chintanu-kumar-3440
Last seen 10.2 years ago
Hi Jim, Thanks ! I tried with the bits you had given. There is a hitch, and not very sure about this error message: > myRMA <- justRMA() Attaching package: 'hgu133plus2cdf' The following object(s) are masked from package:hgu133a2cdf : i2xy, xy2i > probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", + aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") Error in switch(name, Probe = aafProbe(probeids), Symbol = aafSymbol(probeids, : switch: EXPR must return a length 1 vector > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2cdf_2.4.0 hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 affycoretools_1.16.0 hgu133a2cdf_2.4.0 siggenes_1.18.0 [7] multtest_2.0.0 annaffy_1.16.0 KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [13] AnnotationDbi_1.6.0 affy_1.22.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 Category_2.10.0 gcrma_2.16.0 genefilter_1.24.0 GOstats_2.10.0 [8] graph_1.22.2 GSEABase_1.6.0 limma_2.18.0 MASS_7.2-46 preprocessCore_1.6.0 RBGL_1.20.0 RCurl_0.94-1 [15] survival_2.35-4 tools_2.9.0 XML_2.3-0 xtable_1.5-5 > I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs? Not really. R eventually crashes. I have tried 2/3 times. I encounter the crash when I enter the final code: genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) Thanks again ! Cheers, Chintanu ________________________________________ From: James W. MacDonald [jmacdon@med.umich.edu] Sent: 19 May 2009 01:16 To: Sarmah, Chintanu Kumar Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Affy output Hi Chintanu, Sarmah, Chintanu Kumar wrote: > Hi All, > > I am having some trouble to do the annotation of the normalized genes > for a set of Affymetrix files (cdf = HG-U133_Plus_2) using UniGene ID > and then, creating the output table. > > I was mainly referring to the book, "Bioinformatics & Computational > Biology Solutions Using R and Bioinformatics" but at one stage, I was > unsure as to how to proceed. > > Any suggestion would be appreciated. Also, wonder if there is any > other (quicker!) way of doing it ! I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs? Anyway, there are easier ways to do this. One such way is using probes2table() in affycoretools. probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") Best, Jim > > Thank you ! > > Cheers, > > Chintanu > > > >> myRMA <- justRMA() probeids4log2 <- featureNames (myRMA) >> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") anncols >> <- aaf.handler ()[c(1,2,7,9)] anntable4log2 <- aafTableAnn >> (probeids4log2, "hgu133plus2.db", anncols) exprtable4log2 <- >> aafTableInt (myRMA, probeids=probeids4log2) >> table4log2 <- merge >> (anntable4log2, exprtable4log2) >> UniGeneID4log2 <- table4log2$UniGene > # genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) >> sessionInfo () > R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base > packages: [1] splines stats graphics grDevices utils > datasets methods base other attached packages: [1] > hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0 > siggenes_1.18.0 annaffy_1.16.0 KEGG.db_2.2.11 [7] > GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > AnnotationDbi_1.6.0 multtest_2.0.0 affy_1.22.0 [13] > Biobase_2.4.1 loaded via a namespace (and not attached): [1] > affyio_1.12.0 MASS_7.2-46 preprocessCore_1.6.0 > survival_2.35-4 tools_2.9.0 > > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Hi Chintanu, Sarmah, Chintanu Kumar wrote: > Hi Jim, > > Thanks ! > > I tried with the bits you had given. There is a hitch, and not very sure about this error message: > >> myRMA <- justRMA() > > Attaching package: 'hgu133plus2cdf' > > > The following object(s) are masked from package:hgu133a2cdf : > > i2xy, > xy2i > >> probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", > + aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") > > Error in switch(name, Probe = aafProbe(probeids), Symbol = aafSymbol(probeids, : > switch: EXPR must return a length 1 vector Two problems here; this call to probes2table() relies on the position of the arguments being correct, as I am not formally labeling them and I am missing one argument. Second, I need to export aaf.handler() so you can call it directly. Until then you have to load the annaffy package (which you have done, but you have to make sure to do so or you will get the error that aaf.handler() can't be found). probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", anncols = aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "annotated_data") Best, Jim > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.4.0 hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 affycoretools_1.16.0 hgu133a2cdf_2.4.0 siggenes_1.18.0 > [7] multtest_2.0.0 annaffy_1.16.0 KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [13] AnnotationDbi_1.6.0 affy_1.22.0 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 Category_2.10.0 gcrma_2.16.0 genefilter_1.24.0 GOstats_2.10.0 > [8] graph_1.22.2 GSEABase_1.6.0 limma_2.18.0 MASS_7.2-46 preprocessCore_1.6.0 RBGL_1.20.0 RCurl_0.94-1 > [15] survival_2.35-4 tools_2.9.0 XML_2.3-0 xtable_1.5-5 > > > >> I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs? > > Not really. R eventually crashes. I have tried 2/3 times. I encounter the crash when I enter the final code: > > genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) > > > Thanks again ! > > Cheers, > Chintanu > > > ________________________________________ > From: James W. MacDonald [jmacdon at med.umich.edu] > Sent: 19 May 2009 01:16 > To: Sarmah, Chintanu Kumar > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Affy output > > Hi Chintanu, > > Sarmah, Chintanu Kumar wrote: >> Hi All, >> >> I am having some trouble to do the annotation of the normalized genes >> for a set of Affymetrix files (cdf = HG-U133_Plus_2) using UniGene ID >> and then, creating the output table. >> >> I was mainly referring to the book, "Bioinformatics & Computational >> Biology Solutions Using R and Bioinformatics" but at one stage, I was >> unsure as to how to proceed. >> >> Any suggestion would be appreciated. Also, wonder if there is any >> other (quicker!) way of doing it ! > > I'm not sure what trouble you are having - I don't see any error > messages below, so I assume the code runs? > > Anyway, there are easier ways to do this. One such way is using > probes2table() in affycoretools. > > probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", > aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") > > Best, > > Jim > > >> Thank you ! >> >> Cheers, >> >> Chintanu >> >> >> >>> myRMA <- justRMA() probeids4log2 <- featureNames (myRMA) >>> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") anncols >>> <- aaf.handler ()[c(1,2,7,9)] anntable4log2 <- aafTableAnn >>> (probeids4log2, "hgu133plus2.db", anncols) exprtable4log2 <- >>> aafTableInt (myRMA, probeids=probeids4log2) >>> table4log2 <- merge >>> (anntable4log2, exprtable4log2) >>> UniGeneID4log2 <- table4log2$UniGene >> # genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) >>> sessionInfo () >> R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base >> packages: [1] splines stats graphics grDevices utils >> datasets methods base other attached packages: [1] >> hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0 >> siggenes_1.18.0 annaffy_1.16.0 KEGG.db_2.2.11 [7] >> GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 >> AnnotationDbi_1.6.0 multtest_2.0.0 affy_1.22.0 [13] >> Biobase_2.4.1 loaded via a namespace (and not attached): [1] >> affyio_1.12.0 MASS_7.2-46 preprocessCore_1.6.0 >> survival_2.35-4 tools_2.9.0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Hi Jim, Thanks, it is working. And, I appreciate your kind help. Best Wishes, Chintanu ________________________________________ From: James W. MacDonald [jmacdon@med.umich.edu] Sent: 20 May 2009 00:52 To: Sarmah, Chintanu Kumar Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Affy output Hi Chintanu, Sarmah, Chintanu Kumar wrote: > Hi Jim, > > Thanks ! > > I tried with the bits you had given. There is a hitch, and not very sure about this error message: > >> myRMA <- justRMA() > > Attaching package: 'hgu133plus2cdf' > > > The following object(s) are masked from package:hgu133a2cdf : > > i2xy, > xy2i > >> probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", > + aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") > > Error in switch(name, Probe = aafProbe(probeids), Symbol = aafSymbol(probeids, : > switch: EXPR must return a length 1 vector Two problems here; this call to probes2table() relies on the position of the arguments being correct, as I am not formally labeling them and I am missing one argument. Second, I need to export aaf.handler() so you can call it directly. Until then you have to load the annaffy package (which you have done, but you have to make sure to do so or you will get the error that aaf.handler() can't be found). probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", anncols = aaf.handler()[c(1,2,7,9)], html = FALSE, text = TRUE, filename = "annotated_data") Best, Jim > >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133plus2cdf_2.4.0 hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 affycoretools_1.16.0 hgu133a2cdf_2.4.0 siggenes_1.18.0 > [7] multtest_2.0.0 annaffy_1.16.0 KEGG.db_2.2.11 GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [13] AnnotationDbi_1.6.0 affy_1.22.0 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 Category_2.10.0 gcrma_2.16.0 genefilter_1.24.0 GOstats_2.10.0 > [8] graph_1.22.2 GSEABase_1.6.0 limma_2.18.0 MASS_7.2-46 preprocessCore_1.6.0 RBGL_1.20.0 RCurl_0.94-1 > [15] survival_2.35-4 tools_2.9.0 XML_2.3-0 xtable_1.5-5 > > > >> I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs? > > Not really. R eventually crashes. I have tried 2/3 times. I encounter the crash when I enter the final code: > > genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) > > > Thanks again ! > > Cheers, > Chintanu > > > ________________________________________ > From: James W. MacDonald [jmacdon at med.umich.edu] > Sent: 19 May 2009 01:16 > To: Sarmah, Chintanu Kumar > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Affy output > > Hi Chintanu, > > Sarmah, Chintanu Kumar wrote: >> Hi All, >> >> I am having some trouble to do the annotation of the normalized genes >> for a set of Affymetrix files (cdf = HG-U133_Plus_2) using UniGene ID >> and then, creating the output table. >> >> I was mainly referring to the book, "Bioinformatics & Computational >> Biology Solutions Using R and Bioinformatics" but at one stage, I was >> unsure as to how to proceed. >> >> Any suggestion would be appreciated. Also, wonder if there is any >> other (quicker!) way of doing it ! > > I'm not sure what trouble you are having - I don't see any error > messages below, so I assume the code runs? > > Anyway, there are easier ways to do this. One such way is using > probes2table() in affycoretools. > > probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db", > aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data") > > Best, > > Jim > > >> Thank you ! >> >> Cheers, >> >> Chintanu >> >> >> >>> myRMA <- justRMA() probeids4log2 <- featureNames (myRMA) >>> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") anncols >>> <- aaf.handler ()[c(1,2,7,9)] anntable4log2 <- aafTableAnn >>> (probeids4log2, "hgu133plus2.db", anncols) exprtable4log2 <- >>> aafTableInt (myRMA, probeids=probeids4log2) >>> table4log2 <- merge >>> (anntable4log2, exprtable4log2) >>> UniGeneID4log2 <- table4log2$UniGene >> # genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2) >>> sessionInfo () >> R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base >> packages: [1] splines stats graphics grDevices utils >> datasets methods base other attached packages: [1] >> hgu133a2.db_2.2.11 hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0 >> siggenes_1.18.0 annaffy_1.16.0 KEGG.db_2.2.11 [7] >> GO.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 >> AnnotationDbi_1.6.0 multtest_2.0.0 affy_1.22.0 [13] >> Biobase_2.4.1 loaded via a namespace (and not attached): [1] >> affyio_1.12.0 MASS_7.2-46 preprocessCore_1.6.0 >> survival_2.35-4 tools_2.9.0
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