Yesterday I posted this question to the list, but the spam blocker didn't let it through. Below my question is a response from Mark Robinson.
-------------------------------------------------------------------------------------------------------------- Following the example provided at http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array-analysis , I am running the following code: chipType <- "HT_HG-U133A" dataSet = "myData" library(aroma.affymetrix) verbose <- Arguments$getVerbose(-8, timestamp=TRUE) cdf <- AffymetrixCdfFile$byChipType(chipType) cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf) bc <- RmaBackgroundCorrection(cs) csBC <- process(bc,verbose=verbose) qn <- QuantileNormalization(csBC) csN <- process(qn, verbose=verbose) plm <- RmaPlm(csN) fit(plm, verbose=verbose) ces <- getChipEffectSet(plm) gExprs <- extractDataFrame(ces, units=NULL, addNames=TRUE) This seems to be working beautifully. However, I'm doing an analysis that requires my expression values to be summarized at the gene level rather than the probeset level. In the gExprs object that results from the above analysis, I get a data.frame object in which each row contains expression values for a given probeset across all samples. What I would love to see in each row is an expression value for a given gene. I believe RMA has the ability to do this, but I'm not sure how to do it via aroma.affymetrix. Any suggestions? I'm happy to provide any more details that would be helpful. Regards, -Steve -------------------------------------------------------------------------------------------------------------- Hi Steve. As to your question, it depends on what you need. When you say you want every row to be a gene, do you just want to know the gene name that goes with the probeset identifier, or do you want to combine probesets such that all probes for a given gene (by some definition -- RefSeq, Ensembl, etc) are used to arise at the summarize value (a la the MBNI CustomCDF)? If the former, then there are annotation packages within R. If the latter, I have a few cautionary tales of doing this, since the different probesets for a given locus can be measuring different variants. But if you still want to do this, we need to make a CDF file specific to the annotation you want. For the standard HG-U133 arrays, I know the MBNI guys made the CDFs and we could use those within aroma.affymetrix. I don't know if they build custom CDFs for the HT- arrays. Hope that gets you started. Cheers, Mark- Show quoted text - ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
