[BioC] Affy output

[Sarmah, Chintanu Kumar]

Hi Jim,

Thanks !

I tried with the bits you had given. There is a hitch, and not very sure about this error message:

>  myRMA <- justRMA()

Attaching package: 'hgu133plus2cdf'


        The following object(s) are masked from package:hgu133a2cdf :

         i2xy,
         xy2i

> probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db",
+ aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data")

Error in switch(name, Probe = aafProbe(probeids), Symbol = aafSymbol(probeids,  :
  switch: EXPR must return a length 1 vector

> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] hgu133plus2cdf_2.4.0  hgu133a2.db_2.2.11    hgu133plus2.db_2.2.11 affycoretools_1.16.0  hgu133a2cdf_2.4.0     siggenes_1.18.0
 [7] multtest_2.0.0        annaffy_1.16.0        KEGG.db_2.2.11        GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4
[13] AnnotationDbi_1.6.0   affy_1.22.0           Biobase_2.4.1

loaded via a namespace (and not attached):
 [1] affyio_1.12.0        annotate_1.22.0      biomaRt_2.0.0        Category_2.10.0      gcrma_2.16.0         genefilter_1.24.0    GOstats_2.10.0
 [8] graph_1.22.2         GSEABase_1.6.0       limma_2.18.0         MASS_7.2-46          preprocessCore_1.6.0 RBGL_1.20.0          RCurl_0.94-1
[15] survival_2.35-4      tools_2.9.0          XML_2.3-0            xtable_1.5-5



> I'm not sure what trouble you are having - I don't see any error messages below, so I assume the code runs?

Not really. R eventually crashes. I have tried 2/3 times. I encounter the crash when I enter the final code:

genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2)


Thanks again !

Cheers,
Chintanu


________________________________________
From: James W. MacDonald [jmacdon at med.umich.edu]
Sent: 19 May 2009 01:16
To: Sarmah, Chintanu Kumar
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Affy output

Hi Chintanu,

Sarmah, Chintanu Kumar wrote:
> Hi All,
>
> I am having some trouble to do the annotation of the normalized genes
> for a set of Affymetrix files (cdf = HG-U133_Plus_2) using UniGene ID
> and then, creating the output table.
>
> I was mainly referring to the book, "Bioinformatics & Computational
> Biology Solutions Using R and Bioinformatics" but at one stage, I was
> unsure as to how to proceed.
>
> Any suggestion would be appreciated. Also, wonder if there is any
> other (quicker!) way of doing it !

I'm not sure what trouble you are having - I don't see any error
messages below, so I assume the code runs?

Anyway, there are easier ways to do this. One such way is using
probes2table() in affycoretools.

probes2table(myRMA, featureNames(myRMA), "hgu133plus2.db",
aaf.handler()[c(1,2,7,9)], FALSE, TRUE, filename = "annotated_data")

Best,

Jim


>
> Thank you !
>
> Cheers,
>
> Chintanu
>
>
>
>> myRMA <- justRMA() probeids4log2 <- featureNames (myRMA)
>> symbols4log2 <- aafSymbol (probeids4log2, "hgu133plus2.db") anncols
>> <- aaf.handler ()[c(1,2,7,9)] anntable4log2 <- aafTableAnn
>> (probeids4log2, "hgu133plus2.db", anncols) exprtable4log2 <-
>> aafTableInt (myRMA, probeids=probeids4log2)
>>  table4log2 <- merge
>> (anntable4log2, exprtable4log2)
>> UniGeneID4log2 <- table4log2$UniGene
> #  genesANDExpresseion4log2 <- cbind (UniGene=UniGeneID4log2, Log2=table4log2)
>> sessionInfo ()
> R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: attached base
> packages: [1] splines   stats     graphics  grDevices utils
> datasets  methods   base other attached packages: [1]
> hgu133a2.db_2.2.11    hgu133plus2.db_2.2.11 hgu133a2cdf_2.4.0
> siggenes_1.18.0       annaffy_1.16.0        KEGG.db_2.2.11 [7]
> GO.db_2.2.11          RSQLite_0.7-1         DBI_0.2-4
> AnnotationDbi_1.6.0   multtest_2.0.0        affy_1.22.0 [13]
> Biobase_2.4.1 loaded via a namespace (and not attached): [1]
> affyio_1.12.0        MASS_7.2-46          preprocessCore_1.6.0
> survival_2.35-4      tools_2.9.0
>
> [[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
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