On Thu, Dec 11, 2014 at 4:52 AM, Rishi Das Roy <rishi.das...@gmail.com> wrote: > Hi > > Thanks for your reply. I can understand that I can identify alternative > splicing through FIRMA more confidently. However I also want to identify > differentially expressed genes. I have not find any documentation regarding > this in aroma-project.org . > > Please provide any example to find DE genes through aroma.affymetrix.
If you look at http://aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis, you find the following passages: "There are two options, regardless of the kind of custom CDF you use. To fit a summary of the entire transcript (i.e. estimate the overall expression for the transcript), do: plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE) print(plmTr) and then a bit later also: To extract the estimates (transcript or probeset) use either extractMatrix() or extractDataFrame() on the ChipEffectSet that corresponds to the plm object: cesTr <- getChipEffectSet(plmTr) trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE) This will give a data.frame with three rows, each row corresponding to a unit/transcript." Hope this helps Henrik > > Thanks > rishi > > > > On Wednesday, December 10, 2014 11:39:50 PM UTC+2, Henrik Bengtsson wrote: >> >> 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....@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-af...@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-affymetr...@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. -- -- 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. 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