Thanks a lot for the explanation and reference. Rahul
On Oct 10, 11:18 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > > > > > > > > > On Mon, Oct 10, 2011 at 9:01 AM, rahul <v.rahul.sim...@gmail.com> 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 websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://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 aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/