gcrma output id
2
0
Entering edit mode
Dianjing Guo ▴ 90
@dianjing-guo-989
Last seen 11.2 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 • 1.8k views
ADD COMMENT •
0
Entering edit mode
Zhijin Wu ▴ 410
@zhijin-wu-438
Last seen 11.2 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 >
ADD COMMENT •
0
Entering edit mode
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 >> >> >>
ADD REPLY •
0
Entering edit mode
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 > >> > >> > >> > >
ADD REPLY •
0
Entering edit mode
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 >>>> >>>> >>>> >>>> >>>> >> >>
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
Dianjing Guo ▴ 90
@dianjing-guo-989
Last seen 11.2 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 >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >> >>
ADD COMMENT •
0
Entering edit mode
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 > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>> > >>>> > >>>> > >>>> > >> > >> > >
ADD REPLY •
0
Entering edit mode
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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >> >>
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 2173 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6