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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