[BioC] Affy output

[Sarmah, Chintanu Kumar]

Hi Jim,

Thanks, it is working. And, I appreciate your kind help.

Best Wishes,

Chintanu





________________________________________
From: James W. MacDonald [jmacdon at med.umich.edu]
Sent: 20 May 2009 00:52
To: Sarmah, Chintanu Kumar
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Affy output

Hi Chintanu,

Sarmah, Chintanu Kumar wrote:
> 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

Two problems here; this call to probes2table() relies on the position of
the arguments being correct, as I am not formally labeling them and I am
missing one argument. Second, I need to export aaf.handler() so you can
call it directly. Until then you have to load the annaffy package (which
you have done, but you have to make sure to do so or you will get the
error that aaf.handler() can't be found).

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

Best,

Jim


>
>> 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