So with this cdf, and mergeGroups=TRUE, you are getting estimates of the
"transcript cluster" (basically gene) expression -- this is not individual
transcripts of a gene (i.e. isoform) but Affy's definitions of gene. The
relevant identification is the unitName column (the groupName is
irrelevant and in fact misleading when you have summaries of the unit and
not the group -- its always the first group/exon of the unit/gene, so it
doesn't mean anything here). This is Affy's transcript cluster id. In
terms of what you want to do with the id, you have to rely of Affy's
annotation, for example their NetAffx to find out what a transcript
cluster corresponds to.
Best,
Elizabeth
> Hi Henrik,
>
> Here are the code and sessioninfo().
>
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> chipType <- "HuEx-1_0-st-v2"
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="core,A20071112,EP")
> print(cdf)
> cs <- AffymetrixCelSet$byName("GSE16125", cdf=cdf)
> print(cs)
> setCdf(cs,cdf)
> bc <- RmaBackgroundCorrection(cs, tag="core")
> csBC <- process(bc,verbose=verbose)
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> print(qn)
> csN <- process(qn, verbose=verbose)
> plmTr <- ExonRmaPlm(csN, mergeGroups=TRUE)
> print(plmTr)
> fit(plmTr, verbose=verbose)
> rs <- calculateResiduals(plmTr, verbose=verbose)
> cesTr <- getChipEffectSet(plmTr)
> trFit <- extractDataFrame(cesTr, units=1:3, addNames=TRUE)
> trFit_m<-matrix(as.numeric(unlist(trFit[,6:41])),nrow=18708,ncol=36)
>
> The code ran successfully and I got the values as follows.
> unitName groupName unit group cell GSM403456_A195-01 GSM403457_A195-03
> 1 2315251 2315252 1 1 1 18.39242 20.05083
> 2 2315373 2315374 2 1 3 27.54471 37.94356
> 3 2315554 2315586 3 1 7 57.07763 87.79183
>
> I got 18708 rows for the entire transcript.
>
> sessionInfo()
>
> R version 2.10.0 (2009-10-26)
> x86_64-redhat-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] preprocessCore_1.8.0 Biobase_2.6.1 aroma.affymetrix_1.4.0
> [4] aroma.apd_0.1.7 affxparser_1.18.0 R.huge_0.2.0
> [7] aroma.core_1.4.0 aroma.light_1.15.1 matrixStats_0.1.9
> [10] R.rsp_0.3.6 R.filesets_0.7.0 digest_0.4.2
> [13] R.cache_0.2.0 R.utils_1.3.3 R.oo_1.6.7
> [16] affy_1.24.2 R.methodsS3_1.1.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0
>
>
> Thanks,
>
> Anguraj
>
>
> On Feb 21, 2010, at 5:23 PM, Henrik Bengtsson wrote:
>
>> Hi.
>>
>> On Sun, Feb 21, 2010 at 3:24 PM, Anguraj Sadanandam
>> <[email protected]> wrote:
>>> Hi Everyone,
>>>
>>> I have question probably many others using Aroma Affy might have had
>>> the same question. I checked the archive but I couldn't find any
>>> straight forward answer to my question, so I am posting this.
>>>
>>> I used Aroma Affy and successfully processed Human HuEx-1_0-st-v2. I
>>> processed for entire transcript rather than exons. However, I am
>>> struggling to map the group and unit names to gene names. I don't know
>>> if I have to provide any other information.
>>
>> Unit names are defined by the CDF, so which unit names you get depends
>> which CDF you used. Note that the terms 'chip type' and 'CDF' are not
>> the same, cf. Page 'Differences between chip type and chip definition
>> file (CDF)':
>>
>> http://aroma-project.org/definitions/chipTypesAndCDFs.
>>
>> You specified that you've used the 'HuEx-1_0-st-v2' chip type, but you
>> haven't specified which CDF. This is one example why we keep asking
>> everyone to show their scripts and useful verbose output.
>>
>> You are saying you are "struggling", but it is not clear how far
>> you've got and what you have tried this far. Because, I will just
>> point you to the example on Page 'Extract probeset summaries (chip
>> effects) as a data frame':
>>
>> http://aroma-project.org/howtos/extractDataFrame
>>
>> to see if that is a start. Depending on CDF used, that might help
>> you. If you browse the Forum Archives [], you will also find
>> discussions such as:
>>
>> 'questiones about annotations for exon arrays: no gene symbol or
>> refseq id for majority of core probe sets?':
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/ce307bae170c70e8
>>
>> 'Questions about annotations':
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/1f4af7fca4352022
>>
>> /Henrik
>>
>>>
>>> Please let me know.
>>>
>>> Thanks,
>>>
>>> Anguraj
>>>
>>> --
>>> 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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>>
>> --
>> 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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>
> --
> 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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