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 >> >> >