Question: use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis
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gravatar for Michal Okoniewski
10.6 years ago by
Michal Okoniewski190 wrote:
-----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Dan Strumpf Sent: Mon 1/26/2009 10:17 PM To: bioconductor at stat.math.ethz.ch Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis Hello, I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz package (downloaded from http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz )as a cdf source/mapping for processing Human exon array data within 'affy' package. Processing went smoothly without any error messages. Noticed some communication about this package in Oct. 2007, and am not clear if results using it are relaible. I am interested in processing Human exon array data also with gcRMA and am wondering if should use the above package or use xps/exonmap/oligo instead? Would like to know also what are to options for differential expression analysis equivalent to samr limma or RankProd for paired samples from within exon array analysis packages or could the preprocessed/normalized data be exported and used with xps/exonmap/oligo packages. Thanks, Dan ===================================================== Hi Dan, xps uses the "most proper" pgf and bkg Affymetrix annotation, while exonmap gives you more flexibility of playing around with annotations - both require extra database installation effort, but I think it is worth it. Did you run the summarization with this package? I think the discussion in Oct 07 was about the fact that you have to remove some probesets to run RMA... or was it fixed? You can use also the CDFs from X:MAP downloads page - they manage with RMA/plier. Cheers, Michal
annotation cdf limma rankprod • 588 views
ADD COMMENTlink modified 10.7 years ago by Dan Strumpf70 • written 10.6 years ago by Michal Okoniewski190
Answer: use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis
0
gravatar for Dan Strumpf
10.7 years ago by
Dan Strumpf70
Dan Strumpf70 wrote:
Hi Michal, Thanks for your reply and suggestions! Please see my further comments/questions below in UPPER: xps uses the "most proper" pgf and bkg Affymetrix annotation SO THESE WOULD BE WHATEVER AFFYMETRIX IS PROVIDING - NOT REMAPPED FILES, CORRECT? IF YOU'RE FAMILIAR WITH XPS, COULD YOU INDICATE WHERE IN THE DOCUMENTATION THE INITIAL PROCESSING OF EXON ARRAYS (WITH REFERENCE TO THE USE OF PGF AND BKG) IS MENTIONED. , while exonmap gives you more flexibility of playing around with annotations I REALIZE THAT XMAP HAS REMAPPED FILES - both require extra database installation effort, but I think it is worth it. Did you run the summarization with this package? I RUN THE COMPLETE RMA 'PROCESSING' SO THAT INCLUDED SUMMARIZATION. I think the discussion in Oct 07 was about the fact that you have to remove some probesets to run RMA... or was it fixed? I COULD NOT TELL FROM THE COMMUNICATION IF THAT WAS FIXED. BECAUSE I HAD NO ISSUES RUNNING RMA USING THIS CDF PACKAGE, WOULD LIKE TO ASK IF THE AUTHOR OF huex10stv2cdf_1.15.0.tar.gz HAVE FIXED IT You can use also the CDFs from X:MAP downloads page - they manage with RMA/plier. I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'. Cheers, Dan Michal Okoniewski wrote: > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf > Sent: Mon 1/26/2009 10:17 PM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis > > Hello, > > I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz > package (downloaded from > http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz > )as a cdf source/mapping for processing Human exon array data within 'affy' > package. Processing went smoothly without any error messages. Noticed some > communication about this package in Oct. 2007, and am not clear if results > using it are relaible. > I am interested in processing Human exon array data also with gcRMA and am > wondering if should use the above package or use xps/exonmap/oligo instead? > Would like to know also what are to options for differential expression > analysis equivalent to samr limma or RankProd for paired samples from within > exon array analysis packages or could the preprocessed/normalized data be > exported and used with xps/exonmap/oligo packages. > > Thanks, > > Dan > ===================================================== > > Hi Dan, > > xps uses the "most proper" pgf and bkg Affymetrix annotation, while exonmap gives you > more flexibility of playing around with annotations - both require extra database installation > effort, but I think it is worth it. > > Did you run the summarization with this package? I think the discussion in Oct 07 was about > the fact that you have to remove some probesets to run RMA... or was it fixed? > You can use also the CDFs from X:MAP downloads page - they manage with RMA/plier. > > Cheers, > Michal >
ADD COMMENTlink written 10.7 years ago by Dan Strumpf70
Dear Dan As the author of xps please allow me to answer your follow-up questions regarding xps: Michal has already mentioned that xps uses the PGF, CLF and annotation files provided by Affymetrix. However, internally these files are converted to a standard format for xps, so that you need to import these files only once, see the help file ?import.exon.scheme. Regarding the documentation: Although the vignette deals only with the basics, it mentions two files located in subdirectory xps/examples, namely "script4xps.R" and "script4exon.R". Both scripts contain code examples which you mostly need to only copy/paste. File "script4exon.R" uses the Affymetrix human tissue-mixture exon array dataset as an example how to process the HuExon array data as well as the HGU133Plus2 data and the HuGene data. Maybe one note on detection of differential analysis: Although "limma" is surely the preferred package, xps has also functions for filtering of data before further analysis, and for detecting differentially expressed genes, when there are only two groups ( see Chapter 5 of vignette xps.pdf) Please let me know if you have further questions. Best regards Christian Dan Strumpf wrote: > Hi Michal, > > Thanks for your reply and suggestions! Please see my further > comments/questions below in UPPER: > > xps uses the "most proper" pgf and bkg Affymetrix annotation > > SO THESE WOULD BE WHATEVER AFFYMETRIX IS PROVIDING - NOT REMAPPED > FILES, CORRECT? IF YOU'RE FAMILIAR WITH XPS, COULD YOU INDICATE WHERE > IN THE DOCUMENTATION THE INITIAL PROCESSING OF EXON ARRAYS (WITH > REFERENCE TO THE USE OF PGF AND BKG) IS MENTIONED. > > , while exonmap gives you > more flexibility of playing around with annotations > > I REALIZE THAT XMAP HAS REMAPPED FILES > > - both require extra database installation > effort, but I think it is worth it. > > Did you run the summarization with this package? > > I RUN THE COMPLETE RMA 'PROCESSING' SO THAT INCLUDED SUMMARIZATION. > > I think the discussion in Oct 07 was about > the fact that you have to remove some probesets to run RMA... or was > it fixed? > > I COULD NOT TELL FROM THE COMMUNICATION IF THAT WAS FIXED. BECAUSE I > HAD NO ISSUES RUNNING RMA USING THIS CDF PACKAGE, WOULD LIKE TO ASK IF > THE AUTHOR OF huex10stv2cdf_1.15.0.tar.gz HAVE FIXED IT > > You can use also the CDFs from X:MAP downloads page - they manage with > RMA/plier. > > I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB > SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A > FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'. > > Cheers, > Dan > > > Michal Okoniewski wrote: >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf >> Sent: Mon 1/26/2009 10:17 PM >> To: bioconductor at stat.math.ethz.ch >> Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon >> array analysis >> >> Hello, >> >> I am new to exon array analysis and have used the >> huex10stv2cdf_1.15.0.tar.gz package (downloaded from >> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz >> )as a cdf source/mapping for processing Human exon array data within >> 'affy' package. Processing went smoothly without any error messages. >> Noticed some communication about this package in Oct. 2007, and am >> not clear if results using it are relaible. >> I am interested in processing Human exon array data also with gcRMA >> and am wondering if should use the above package or use >> xps/exonmap/oligo instead? Would like to know also what are to >> options for differential expression analysis equivalent to samr limma >> or RankProd for paired samples from within exon array analysis >> packages or could the preprocessed/normalized data be exported and >> used with xps/exonmap/oligo packages. >> >> Thanks, >> >> Dan >> ===================================================== >> >> Hi Dan, >> >> xps uses the "most proper" pgf and bkg Affymetrix annotation, while >> exonmap gives you >> more flexibility of playing around with annotations - both require >> extra database installation >> effort, but I think it is worth it. >> >> Did you run the summarization with this package? I think the >> discussion in Oct 07 was about >> the fact that you have to remove some probesets to run RMA... or was >> it fixed? >> You can use also the CDFs from X:MAP downloads page - they manage >> with RMA/plier. >> >> Cheers, >> Michal > > _______________________________________________ > 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 > >
ADD REPLYlink written 10.6 years ago by cstrato3.9k
Dear Christian, Thanks for clarifying those points about xps. I'll look up the example scripts and will follow-up with you as needed. Cheers, Dan cstrato wrote: > Dear Dan > > As the author of xps please allow me to answer your follow-up questions > regarding xps: > > Michal has already mentioned that xps uses the PGF, CLF and annotation > files provided by Affymetrix. However, internally these files are > converted to a standard format for xps, so that you need to import these > files only once, see the help file ?import.exon.scheme. > > Regarding the documentation: > Although the vignette deals only with the basics, it mentions two files > located in subdirectory xps/examples, namely "script4xps.R" and > "script4exon.R". Both scripts contain code examples which you mostly > need to only copy/paste. > > File "script4exon.R" uses the Affymetrix human tissue-mixture exon array > dataset as an example how to process the HuExon array data as well as > the HGU133Plus2 data and the HuGene data. > > Maybe one note on detection of differential analysis: > Although "limma" is surely the preferred package, xps has also functions > for filtering of data before further analysis, and for detecting > differentially expressed genes, when there are only two groups ( see > Chapter 5 of vignette xps.pdf) > > Please let me know if you have further questions. > > Best regards > Christian > > > Dan Strumpf wrote: >> Hi Michal, >> >> Thanks for your reply and suggestions! Please see my further >> comments/questions below in UPPER: >> >> xps uses the "most proper" pgf and bkg Affymetrix annotation >> >> SO THESE WOULD BE WHATEVER AFFYMETRIX IS PROVIDING - NOT REMAPPED >> FILES, CORRECT? IF YOU'RE FAMILIAR WITH XPS, COULD YOU INDICATE WHERE >> IN THE DOCUMENTATION THE INITIAL PROCESSING OF EXON ARRAYS (WITH >> REFERENCE TO THE USE OF PGF AND BKG) IS MENTIONED. >> >> , while exonmap gives you >> more flexibility of playing around with annotations >> >> I REALIZE THAT XMAP HAS REMAPPED FILES >> >> - both require extra database installation >> effort, but I think it is worth it. >> >> Did you run the summarization with this package? >> >> I RUN THE COMPLETE RMA 'PROCESSING' SO THAT INCLUDED SUMMARIZATION. >> >> I think the discussion in Oct 07 was about >> the fact that you have to remove some probesets to run RMA... or was >> it fixed? >> >> I COULD NOT TELL FROM THE COMMUNICATION IF THAT WAS FIXED. BECAUSE I >> HAD NO ISSUES RUNNING RMA USING THIS CDF PACKAGE, WOULD LIKE TO ASK IF >> THE AUTHOR OF huex10stv2cdf_1.15.0.tar.gz HAVE FIXED IT >> >> You can use also the CDFs from X:MAP downloads page - they manage with >> RMA/plier. >> >> I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB >> SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A >> FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'. >> >> Cheers, >> Dan >> >> >> Michal Okoniewski wrote: >>> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf >>> Sent: Mon 1/26/2009 10:17 PM >>> To: bioconductor at stat.math.ethz.ch >>> Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon >>> array analysis >>> >>> Hello, >>> >>> I am new to exon array analysis and have used the >>> huex10stv2cdf_1.15.0.tar.gz package (downloaded from >>> http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz >>> )as a cdf source/mapping for processing Human exon array data within >>> 'affy' package. Processing went smoothly without any error messages. >>> Noticed some communication about this package in Oct. 2007, and am >>> not clear if results using it are relaible. >>> I am interested in processing Human exon array data also with gcRMA >>> and am wondering if should use the above package or use >>> xps/exonmap/oligo instead? Would like to know also what are to >>> options for differential expression analysis equivalent to samr limma >>> or RankProd for paired samples from within exon array analysis >>> packages or could the preprocessed/normalized data be exported and >>> used with xps/exonmap/oligo packages. >>> >>> Thanks, >>> >>> Dan >>> ===================================================== >>> >>> Hi Dan, >>> >>> xps uses the "most proper" pgf and bkg Affymetrix annotation, while >>> exonmap gives you >>> more flexibility of playing around with annotations - both require >>> extra database installation >>> effort, but I think it is worth it. >>> >>> Did you run the summarization with this package? I think the >>> discussion in Oct 07 was about >>> the fact that you have to remove some probesets to run RMA... or was >>> it fixed? >>> You can use also the CDFs from X:MAP downloads page - they manage >>> with RMA/plier. >>> >>> Cheers, >>> Michal >> >> _______________________________________________ >> 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 >> >> >
ADD REPLYlink written 10.6 years ago by Dan Strumpf70
Hi Dan, > You can use also the CDFs from X:MAP downloads page - they manage with > RMA/plier. > > I WAS CONSIDERING THAT, BUT WASN'T SURE IF I'LL STILL NEED THE DB > SETUP FOR GETTING THE 'REMAPPED' ANNOTATION, OR WHETHER I COULD GET A > FLAT FILE THAT I COULD USE TO ANNOTATE 'EXTERNALLY'. > > Cheers, > Dan The cdf available at X:MAP page does not in fact require the whole X:MAP database to run. You can use read.exon(), attach the CDF to the AffyBatch, call RMA/plier and do pairwise comparison without connecting to the DB - you'll get eSet with the vast majority of Affy exon probesets. However all the other functionality of exonmap: annotation translating, filtering, visualization - do a lot of X:MAP queries in mysql. This functionality you can also use on the data processed with other packages (eg xps) or imported from outside. My hint for doing data mining with exon arrays is to use in parallel: exonmap and X:MAP browser and perhaps sometimes Ensembl and other databases to see transcripts, isoforms and exons and their expression profiles. But this is at the stage of "deeper insight" after the summarization and filtering. The other questions have been answered already by Christian and Jim :) Thanks! Best, Michal
ADD REPLYlink written 10.6 years ago by Michal Okoniewski50
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