Hi.
On Thu, Jul 14, 2011 at 10:25 AM, sean nj <njs...@gmail.com> wrote:
> 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.
Thanks. I've fixed this so that extractExpressionSet() now by default
returns log2 signals. Before they returned non-logged signals. Just
run (once):
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
and you'll get the corrected version.
>
> 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")
This is really a question for Bioconductor, or plain R, because from
here you have an ExpressionSet object. Anyhow, you probably want to
look at the help for argument 'check.names' of read.table(), because I
think it is when you read your file back in you get the conversion.
The file itself is probably correct.
Hope this helps
/Henrik
>
>
> 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.
>>
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>> > 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.
>
>
> You received this message because you are subscribed to the Google Groups
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> 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/
>
--
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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