Hi Henrik, I am sorry to bother you again.
My question is what the format of probe values in the eset? Are they the direct normalized intensity value or log tranformed? I asked this question because I got very high logFC values after limma analysis. I googled and people mentioned that lmFit expects log transformed intensity value. Another question, is there a way to export RMA normalized dataset as a table? I did something like the following to get a table, but I am not sure if it's the right way. And in the table I got, there is a prefix X to all probes (for example X6733_at for the original probe 6733_at). >write.table(eset,"Gastric_ENTREZG_wide.txt",sep="\t") > write.table(t(read.table("Gastric_ENTREZG_wide.txt",sep > ="\t")),"Gastric_ENTREZG_tall.txt",sep="\t") Thanks a lot, Ying On Jul 9, 10:09 pm, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > On Fri, Jul 8, 2011 at 7:33 AM, sean nj <njs...@gmail.com> wrote: > > Hi guys, > > > I am new to the aroma.affymetrix package. > > [snip] > > > One more question, is there a Vignette/instruction to illustrate the > > further gene expression analysis (high-level analysis?) using the > > output of aroma.affymetrix's RMA analysis? Or what's the usual gene > > expression data analysis work flow (starting with aroma.affymetrix)? > > You want to turn to the limma package (or other Bioconductor > solutions) for "downstream" gene expression analysis. In order to do > this, you need to get the RMA gene-expression summaries as an > ExpressionSet object (which a class defined in the Biobase package of > Bioconductor). When you run the RMA pipeline in aroma.affymetrix > you'll end up with a so called ChipEffectSet. The > extractExpressionSet() method (*** see below***) will do what you > need, e.g. > > > ces <- doRMA("My_Met_Melanoma", chipType="HG-U133_Plus_2,Hs_ENTREZG", > > verbose=-5); > > ces > > ChipEffectSet: > Name: My_Met_Melanoma > Tags: RBC,QN,RMA > Path: plmData/My_Met_Melanoma,RBC,QN,RMA/HG-U133_Plus_2 > Platform: Affymetrix > Chip type: HG-U133_Plus_2,Hs_ENTREZG,monocell > ...> eset <- extractExpressionSet(ces, verbose=-5); > > eset > > ExpressionSet (storageMode: lockedEnvironment) > assayData: 54675 features, 6 samples > element names: exprs > protocolData: none > phenoData: none > featureData: none > experimentData: use 'experimentData(object)' > Annotation: > > See also how-to page 'Extract probeset summaries (chip effects) as a > 'Biobase' ExpressionSet object': > > http://aroma-project.org/howtos/extractExpressionSet > > After the above steps, turn to limma. For example, the following > dummy example is adopted from 'limma: Linear Models for Microarray > Data User's Guide': > > > library("limma"); > > design <- cbind(WT=1, MUvsWT=c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE)); > > fit <- lmFit(eset, design); > > fit <- eBayes(fit); > > topTable(fit, coef="MUvsWT"); > > and so on. > > (***) In order to use extractExpressionSet() you need to do install > the latest patches of aroma.affymetrix, which you simply do by: > > source("http://aroma-project.org/hbLite.R"); > hbInstall("aroma.affymetrix"); > > Hope this helps > > Henrik > > > > > Thanks a lot for the help! > > > Ying > > [snip] > > > > >> sessionInfo() > > R version 2.13.0 (2011-04-13) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 > > [3] LC_MONETARY=English_United States.1252 > > LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods > > base > > > other attached packages: > > [1] aroma.affymetrix_2.1.0 aroma.apd_0.1.8 > > affxparser_1.24.0 R.huge_0.2.2 > > [5] aroma.core_2.1.0 aroma.light_1.20.0 > > matrixStats_0.2.2 R.rsp_0.5.4 > > [9] R.cache_0.4.2 R.filesets_1.0.2 > > digest_0.5.0 R.utils_1.7.5 > > [13] R.oo_1.8.0 R.methodsS3_1.2.1 > > > loaded via a namespace (and not attached): > > [1] tools_2.13.0 > > > -- > > 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 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/- > > Hide quoted text - > > - Show quoted text - -- 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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