Hi, you cannot use RMA on exon-arrays, you will need to use exon-aware method such as FIRMA (e.g. http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis).
Hope this helps Henrik PS. For http://aroma-project.org/replication/RMA, I've updated it to use `theta <- extractTheta(ces)` instead of `theta <- extractMatrix(ces)`. This will allow you to set the row names. But as you'll find out, 'theta' becomes an JxKxI array for exon-arrays, where J is the number of genes, I is the number of samples and K is the maximum number of exons per gene found. In other words, using doRMA() on exon arrays gives you at best exon-specific estimates (and they are not very good estimates - FIRMA is doing a much better job on that). On Wed, Dec 10, 2014 at 1:51 AM, Rishi Das Roy <rishi.das...@gmail.com> wrote: > Hi, > > I was trying to perform RMA on Mouse Exon 1.0 ST Array as described in aroma > website (link) using custom cdf MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf.gz . > > I have executed following code in R > > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR") > cs <- AffymetrixCelSet$byName("data_CEL", cdf=cdf); > bc <- RmaBackgroundCorrection(cs); > csB <- process(bc); > qn <- QuantileNormalization(csB, typesToUpdate="pm"); > csN <- process(qn); > plm <- RmaPlm(csN); > fit(plm); > ces <- getChipEffectSet(plm); > theta <- extractMatrix(ces); > rownames(theta) <- getUnitNames(cdf); > Error in `rownames<-`(`*tmp*`, value = c("6838637", "6992377", "6901592", : > length of 'dimnames' [1] not equal to array extent > > Please help me to understand this error and how can I solve this. The > session info is given below. > > With regards > Rishi > > R version 3.1.2 (2014-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=fi_FI.UTF-8 LC_NUMERIC=C LC_TIME=en_GB > LC_COLLATE=en_GB LC_MONETARY=fi_FI.UTF-8 > [6] LC_MESSAGES=en_GB LC_PAPER=en_GB LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] preprocessCore_1.28.0 aroma.light_2.2.0 > aroma.affymetrix_2.12.8 aroma.core_2.12.8 > [5] R.devices_2.12.0 R.filesets_2.6.0 > R.utils_1.34.0 R.oo_1.18.2 > [9] R.methodsS3_1.6.2 affxparser_1.38.0 > pd.moex10st.mm.aceviewg_0.0.1 affy_1.44.0 > [13] BiocInstaller_1.16.1 pd.moex.1.0.st.v1_3.10.0 > RSQLite_1.0.0 DBI_0.3.1 > [17] moex10stmmrefseqcdf_19.0.0 AnnotationDbi_1.28.1 > GenomeInfoDb_1.2.3 oligo_1.30.0 > [21] Biostrings_2.34.0 XVector_0.6.0 > IRanges_2.0.0 S4Vectors_0.4.0 > [25] Biobase_2.26.0 oligoClasses_1.28.0 > BiocGenerics_0.12.1 > > loaded via a namespace (and not attached): > [1] affyio_1.34.0 aroma.apd_0.5.0 base64enc_0.1-2 > bit_1.1-12 codetools_0.2-8 digest_0.6.5 > [7] DNAcopy_1.40.0 ff_2.2-13 foreach_1.4.2 > GenomicRanges_1.18.3 iterators_1.0.7 matrixStats_0.12.2 > [13] PSCBS_0.43.0 R.cache_0.11.0 R.huge_0.8.0 > R.rsp_0.19.6 splines_3.1.2 tools_3.1.2 > [19] zlibbioc_1.12.0 > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
