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.
>
>
> 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.
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