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
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>
--
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
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