[BioC] Exporting in XPS

[cstrato]

Dear Giovanni,

You can use function "export.expr()" which allows you to select the 
annotation you want using parameter "varlist". By default it is set to 
'varlist="*"' which will export all annotation data. However, this will 
result in a huge file in the case of exon arrays, especially when using 
probesets. See the help file "?export.expr"

For the transcript data "rma.tc.core" you can do:

ds.tc <- export.expr(rma.tc.core, treetype="mdp", 
varlist="fUnitName:fTranscriptID:fSymbol:fLevel", 
outfile="MixExon_tc.txt", as.dataframe=TRUE)

colnames(ds.tc)

pheno.tc <- ds.tc[,c("UnitName", "TranscriptID", "GeneSymbol")]

expr.tc <- log2(ds.tc[,5:ncol(ds.tc)])
rownames(expr.tc) <- ds.tc[,"UnitName"]

Here I have split the data into the annotation file "pheno.tc" and the 
log2 expression part "expr.tc".

Now you can for example use both "pheno.tc" and "expr.tc" for package 
"limma".

Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 7/25/12 7:02 PM, Lavorgna Giovanni wrote:
> Dear all,
>
> before applying any filter to Exon data, I would like to export them to a text file as transcripts, i.e, I have RMAed my data using the following command following the code coming along with the package:
>
> rma.tc.core <- rma(data.exon, "MixExonRMAcore", filedir=outdir, tmpdir="", background="antigenomic", normalize=TRUE, option="transcript", exonlevel="affx+core")
>
> Is there a way to get an output like the following (also non log2 trasformed data will suffice):
>
> GeneID  HCC1187 SUM44PE MCF7    MDAMB436        LY2     BT549
> A1BG    6.31    6.35    6.66    6.47    6.81    6.66
> A2M     4.37    4.58    4.57    4.44    4.84    4.47
> A2ML1   5.50    5.85    5.54    5.53    5.60    5.31
> A3GALT2 6.13    6.10    6.06    6.23    5.99    5.76
>
> Thanks in advance.
>
> Giovanni
>
>
>
>
>
> -----------------------------------------------------------
> Giovanni Lavorgna
> DIBIT-HSR
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> Fax: +39-02-2643-4767
> Email: giovanni.lavorgna  at hsr.it
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