gcrma output id
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Dianjing Guo ▴ 90
@dianjing-guo-989
Last seen 10.2 years ago
When i use gcrma to normalize my data, the result output gives id that doesn't match with affy_id. Anyone can point out how to match the id to my genes on affy chip? Thanks, Dianjine
affy gcrma affy gcrma • 1.6k views
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Zhijin Wu ▴ 410
@zhijin-wu-438
Last seen 10.2 years ago
the rownames of exprs(gcrma_output) should be the affy_id On Tue, 2 Nov 2004, Dianjing Guo wrote: > When i use gcrma to normalize my data, the result output gives id that > doesn't match with affy_id. Anyone can point out how to match the id to > my genes on affy chip? > > Thanks, > Dianjine > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
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No that's not the case. I'm using yeast ygs98 chip and the ids should be smaller than 9335. But what i got from gcrma are strange ids like 190400, 189866, 190402 etc. Thanks, Dianjing Zhijin Wu wrote: >the rownames of exprs(gcrma_output) should be the affy_id > > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > >>When i use gcrma to normalize my data, the result output gives id that >>doesn't match with affy_id. Anyone can point out how to match the id to >>my genes on affy chip? >> >>Thanks, >>Dianjine >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >>
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That is strange. GCRMA does not generate its own ids. What affy ids do you get when you use geneNames(your AffyBatch object)? On Tue, 2 Nov 2004, Dianjing Guo wrote: > No that's not the case. I'm using yeast ygs98 chip and the ids should be > smaller than 9335. But what i got from gcrma are strange ids like > 190400, 189866, 190402 etc. > > Thanks, > Dianjing > > Zhijin Wu wrote: > > >the rownames of exprs(gcrma_output) should be the affy_id > > > > > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > > > > > >>When i use gcrma to normalize my data, the result output gives id that > >>doesn't match with affy_id. Anyone can point out how to match the id to > >>my genes on affy chip? > >> > >>Thanks, > >>Dianjine > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor@stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >> > >> > >
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I get regular yeast affy_ids such as : [8440] "9164_at" "9165_at" "9166_at" [9268] "9992_at" "9993_at" "9994_at" D. Zhijin Wu wrote: >That is strange. GCRMA does not generate its own ids. >What affy ids do you get when you use geneNames(your AffyBatch object)? > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > >>No that's not the case. I'm using yeast ygs98 chip and the ids should be >>smaller than 9335. But what i got from gcrma are strange ids like >>190400, 189866, 190402 etc. >> >>Thanks, >>Dianjing >> >>Zhijin Wu wrote: >> >> >> >>>the rownames of exprs(gcrma_output) should be the affy_id >>> >>> >>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>> >>> >>> >>> >>> >>>>When i use gcrma to normalize my data, the result output gives id that >>>>doesn't match with affy_id. Anyone can point out how to match the id to >>>>my genes on affy chip? >>>> >>>>Thanks, >>>>Dianjine >>>> >>>>_______________________________________________ >>>>Bioconductor mailing list >>>>Bioconductor@stat.math.ethz.ch >>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> >>>> >>>> >>>> >>>> >> >>
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Dianjing Guo wrote: > I get regular yeast affy_ids such as : > [8440] "9164_at" "9165_at" "9166_at" > [9268] "9992_at" "9993_at" "9994_at" > > D. I don't see this error using gcrma on yeast chips. > dat <- read.affybatch(filenames=list.celfiles()) > library(gcrma) Loading required package: matchprobes > eset <- gcrma(dat) [snip] > all.equal(row.names(exprs(eset)), geneNames(dat)) [1] TRUE > packageDescription("gcrma", field="Version") [1] "1.1.1" > cdfName(dat) [1] "YG_S98" Are you using a current version of gcrma? Best, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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Dianjing Guo ▴ 90
@dianjing-guo-989
Last seen 10.2 years ago
i just tried rma and it gives normal affy_id. Dianjing Zhijin Wu wrote: >Would you do me one favor of trying rma instead of gcrma and see what ids >you get? Thank you! > > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > >>I get regular yeast affy_ids such as : >>[8440] "9164_at" "9165_at" "9166_at" >>[9268] "9992_at" "9993_at" "9994_at" >> >>D. >> >>Zhijin Wu wrote: >> >> >> >>>That is strange. GCRMA does not generate its own ids. >>>What affy ids do you get when you use geneNames(your AffyBatch object)? >>> >>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>> >>> >>> >>> >>> >>>>No that's not the case. I'm using yeast ygs98 chip and the ids should be >>>>smaller than 9335. But what i got from gcrma are strange ids like >>>>190400, 189866, 190402 etc. >>>> >>>>Thanks, >>>>Dianjing >>>> >>>>Zhijin Wu wrote: >>>> >>>> >>>> >>>> >>>> >>>>>the rownames of exprs(gcrma_output) should be the affy_id >>>>> >>>>> >>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>When i use gcrma to normalize my data, the result output gives id that >>>>>>doesn't match with affy_id. Anyone can point out how to match the id to >>>>>>my genes on affy chip? >>>>>> >>>>>>Thanks, >>>>>>Dianjine >>>>>> >>>>>>_______________________________________________ >>>>>>Bioconductor mailing list >>>>>>Bioconductor@stat.math.ethz.ch >>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >> >>
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This is surprising since gcrma calls rma after its background correction step. Would you provide me your code calling gcrma and maybe one array of your data so I can try it? On Tue, 2 Nov 2004, Dianjing Guo wrote: > i just tried rma and it gives normal affy_id. > > Dianjing > > Zhijin Wu wrote: > > >Would you do me one favor of trying rma instead of gcrma and see what ids > >you get? Thank you! > > > > > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > > > > > >>I get regular yeast affy_ids such as : > >>[8440] "9164_at" "9165_at" "9166_at" > >>[9268] "9992_at" "9993_at" "9994_at" > >> > >>D. > >> > >>Zhijin Wu wrote: > >> > >> > >> > >>>That is strange. GCRMA does not generate its own ids. > >>>What affy ids do you get when you use geneNames(your AffyBatch object)? > >>> > >>>On Tue, 2 Nov 2004, Dianjing Guo wrote: > >>> > >>> > >>> > >>> > >>> > >>>>No that's not the case. I'm using yeast ygs98 chip and the ids should be > >>>>smaller than 9335. But what i got from gcrma are strange ids like > >>>>190400, 189866, 190402 etc. > >>>> > >>>>Thanks, > >>>>Dianjing > >>>> > >>>>Zhijin Wu wrote: > >>>> > >>>> > >>>> > >>>> > >>>> > >>>>>the rownames of exprs(gcrma_output) should be the affy_id > >>>>> > >>>>> > >>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote: > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>>>When i use gcrma to normalize my data, the result output gives id that > >>>>>>doesn't match with affy_id. Anyone can point out how to match the id to > >>>>>>my genes on affy chip? > >>>>>> > >>>>>>Thanks, > >>>>>>Dianjine > >>>>>> > >>>>>>_______________________________________________ > >>>>>>Bioconductor mailing list > >>>>>>Bioconductor@stat.math.ethz.ch > >>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>> > >>>> > >>>> > >>>> > >> > >> > >
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I just tried with two of my cel files and the results seems to be correct. The problem happens only when i try to normalize 60 chips together. Does it mean it has limits requirement? Or something is wrong with any of my particular cel file? Thanks, Dianjing Zhijin Wu wrote: >This is surprising since gcrma calls rma after its background correction >step. Would you provide me your code calling gcrma and maybe one array >of your data so I can try it? > >On Tue, 2 Nov 2004, Dianjing Guo wrote: > > > >>i just tried rma and it gives normal affy_id. >> >>Dianjing >> >>Zhijin Wu wrote: >> >> >> >>>Would you do me one favor of trying rma instead of gcrma and see what ids >>>you get? Thank you! >>> >>> >>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>> >>> >>> >>> >>> >>>>I get regular yeast affy_ids such as : >>>>[8440] "9164_at" "9165_at" "9166_at" >>>>[9268] "9992_at" "9993_at" "9994_at" >>>> >>>>D. >>>> >>>>Zhijin Wu wrote: >>>> >>>> >>>> >>>> >>>> >>>>>That is strange. GCRMA does not generate its own ids. >>>>>What affy ids do you get when you use geneNames(your AffyBatch object)? >>>>> >>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>>No that's not the case. I'm using yeast ygs98 chip and the ids should be >>>>>>smaller than 9335. But what i got from gcrma are strange ids like >>>>>>190400, 189866, 190402 etc. >>>>>> >>>>>>Thanks, >>>>>>Dianjing >>>>>> >>>>>>Zhijin Wu wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>>the rownames of exprs(gcrma_output) should be the affy_id >>>>>>> >>>>>>> >>>>>>>On Tue, 2 Nov 2004, Dianjing Guo wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>>When i use gcrma to normalize my data, the result output gives id that >>>>>>>>doesn't match with affy_id. Anyone can point out how to match the id to >>>>>>>>my genes on affy chip? >>>>>>>> >>>>>>>>Thanks, >>>>>>>>Dianjine >>>>>>>> >>>>>>>>_______________________________________________ >>>>>>>>Bioconductor mailing list >>>>>>>>Bioconductor@stat.math.ethz.ch >>>>>>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >> >>
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