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 . <http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fvignettes%2FFIRMA-HumanExonArrayAnalysis&sa=D&sntz=1&usg=AFQjCNE_MgdlrbV_N3Pb50439vC9YF1P6g>
Please provide any example to find DE genes through aroma.affymetrix. 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 > <http://www.google.com/url?q=http%3A%2F%2Faroma-project.org%2Fvignettes%2FFIRMA-HumanExonArrayAnalysis&sa=D&sntz=1&usg=AFQjCNE_MgdlrbV_N3Pb50439vC9YF1P6g>). > > > > 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 > <javascript:>> 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 > <javascript:> > > 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 <javascript:>. > > 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.
