Hi, I'll leave the details to FIRMA experts, but you are using really large values of argument 'ram'. It might be that you ran out of memory (the you got an error message). If you used cut'n'paste, instead of source(), to do the analysis, it might be that one of the fit() methods was preemptively finished. If so, not all units have been fitted. Rerun with ram=1 to see if you get a different result; the units already fitted will be skipped.
I'm also not sure if > 431210/(1190297*107) [1] 0.003385710 is an exceptionally large fraction. Note also that 431210/107 is exactly 4030; it could be that it is the exact same 4030 units that are NA in all samples. That could be explained by some units are not fitted or are Affymetrix control units. BTW, not all methods take argument 'ram'. Instead, use the global aroma settings for achieving the same, e.g. setOption(aromaSettings, "memory/ram", 50). More info at http://aroma-project.org/settings. This way your scripts are clean and can be ran "as-is" on other machines with less memory. Maybe this helps(?) /Henrik On Mon, Aug 2, 2010 at 7:24 PM, Adi Tarca <ata...@med.wayne.edu> wrote: > Hi all, > I have a batch of 107 mice exon arrays for which I computed FIRMA > scores and I got many NaN, Inf and 0 values which disable further > analysis based on log FIRMA values for some probesets. I was wondering > if this is a known issue or I am the only one to get these results. > > > Here is the code I use to get the FIRMA scores: > > library(aroma.affymetrix) > verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > chipType <- "MoEx-1_0-st-v1" > cdf <- AffymetrixCdfFile$byChipType(chipType, > tags="fullR1,A20080718,MR") > cs <- AffymetrixCelSet$byName("mice2010", cdf=cdf) > bc <- RmaBackgroundCorrection(cs, tag="fullR1,A20080718,MR") > csBC <- process(bc,verbose=verbose,ram=500) > qn <- QuantileNormalization(csBC, typesToUpdate="pm") > csN <- process(qn, verbose=verbose,ram=500) > plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) > fit(plmTr, verbose=verbose,ram=500) > > firma <- FirmaModel(plmTr) > fit(firma, verbose=verbose,ram=500) > fs <- getFirmaScores(firma) > myres2=extractDataFrame(fs,addNames=FALSE) > myres=as.matrix(myres2[,-(1:3)]) > > > Here is the counts of NaN Inf and 0 values: > >> dim(myres) > [1] 1190297 107 >> sum(is.nan(myres)) > [1] 431210 >> sum(is.infinite(myres),na.rm=TRUE) > [1] 855 >> sum(myres==0,na.rm=TRUE) > [1] 214 > > > > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] aroma.affymetrix_1.5.0 aroma.apd_0.1.7 > affxparser_1.20.0 > [4] R.huge_0.2.0 aroma.core_1.5.0 > aroma.light_1.16.0 > [7] matrixStats_0.2.1 R.rsp_0.3.6 > R.cache_0.3.0 > [10] R.filesets_0.8.1 digest_0.4.2 > R.utils_1.4.0 > [13] R.oo_1.7.2 R.methodsS3_1.2.0 > > > > > > > > > > > > > > > > -- > 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/ > -- 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/
