Hi. On Mon, Oct 10, 2011 at 9:01 AM, rahul <[email protected]> wrote: > Hello Henrik, > > I am using the follwing commands to process my data. > > library(aroma.affymetrix) > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > chipType <- "HuEx-1_0-st-v2" > cdf <- AffymetrixCdfFile$byChipType(chipType, tag="web,v_cdf") > print(cdf) > cs <- AffymetrixCelSet$byName("Sample", cdf=cdf) > print(cs) > setCdf(cs, cdf) > bc <- RmaBackgroundCorrection(cs, tag="web,v_cdf") > csBC <- process(bc,verbose=verbose) > qn <- QuantileNormalization(csBC, typesToUpdate="pm") > print(qn) > csN <- process(qn, verbose=verbose) > plmEx <- ExonRmaPlm(csN, mergeGroups=FALSE) > print(plmEx) > fit(plmEx, verbose=verbose) > cesEx <- getChipEffectSet(plmEx) > trFit <- extractDataFrame(cesEx, addNames=TRUE) > > My question: the resulting data frame (trFit) has values in regular > scale(same scale as intensity values in .cel files). I expected them > to be in log2 scale. Did i miss a step or we get the values only in > the regular scale.
Yes, this is correct. In the Aroma framework, all data/signals are (intentionally) stored on the original scale, with one of the reasons being that negative and zero signal estimates cannot be represented on the log scale. The original/intensity scale is simply the most generic one. Note that parameters may still have been estimated on say the log2 scale, but before being saved they are backtransformed to the original scale. It's been awhile, but there has been some more posts/discussion on this back in time. You need to log2() yourself, e.g. vignette 'Using the GenomeGraphs package with FIRMA' [http://aroma-project.org/node/61]. /Henrik > > -- > 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 with website http://www.aroma-project.org/. > To post to this group, send email to [email protected] > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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 with website http://www.aroma-project.org/. To post to this group, send email to [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
