Hoon, thanks for the note. Yes, there is a discrepancy in how clever
the methods are. Basically the AromaUnit<Nnn>CnBinarySet methods go
further in trying to figure out what annotations are needed. FYI,
contrary to data set directories, the name of the chip type directory
will never have tags, which is why the files end up in:
plmData/AffyTestData,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6/
and not
plmData/AffyTestData,ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY/GenomeWideSNP_6,Full/
regardless of CDF annotation you used This was an active design
decision by us (which for various reasons would be too lengthy to get
into here).
To achieve some consistency with how you setup the AffymetrixCelSet, you can do:
dataSet <- "AffyTestData";
chipType <- "GenomeWideSNP_6";
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
csR <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
cesN <- CnChipEffectSet$byName(dataSet,
tags="ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY", cdf=cdf);
FYI, to speed up the latter, you can help out and specify arguments
'combineAlleles=FALSE' and 'mergeStrands=TRUE' (these correspond to
your doCRMAv2() call below).
/Henrik
On Fri, Nov 11, 2011 at 8:55 AM, wisekh6 <wise...@gmail.com> wrote:
> Dear Pierre,
>
> Thank you very much for your prompt reply.
>
> FYI. I processed the Affymetrix SNP 6.0 data as follows:
> ---------------------------------------------------------------------------------
> dataSet <-"AffyTestData"
> chipType <-"GenomeWideSNP_6"
> verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
> cdf <-AffymetrixCdfFile$byChipType(chipType, tags="Full");
> csR <-AffymetrixCelSet$byName(dataSet, cdf=cdf);
> ds <- doCRMAv2(csR, cdf=cdf, combineAlleles=FALSE,
> verbose=verbose);
> --------------------------------------------------------------------------------
>
>
> Then, I could access total and fracB data with the following scripts :
> --------------------------------------------------------------------------------
> dsTotal <- AromaUnitTotalCnBinarySet$byName(dataSet, tags="ACC,ra,-
> XY,BPN,-XY,AVG,FLN,-XY", chipType=chipType);
> dsFracB <- AromaUnitFracBCnBinarySet$byName(dataSet, tags="ACC,ra,-
> XY,BPN,-XY,AVG,FLN,-XY", chipType=chipType)
> --------------------------------------------------------------------------------
>
> However, I couldn't access a chip effect set with:
> cesN <- CnChipEffectSet$byName(dataSet,tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType=chipType)
>
> And, as you know, it worked when I used "GenomeWideSNP_6.Full" as a
> chip type:
> cesN <- CnChipEffectSet$byName(dataSet,tags="ACC,ra,-XY,BPN,-
> XY,AVG,FLN,-XY", chipType=paste(chipType,",Full",sep=""))
>
>
> Thank you,
>
> Hoon
>
>
> On Nov 11, 3:42 am, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
>> Hi wisekh6,
>>
>> Although you don't give the code you used to process this data, from
>> what you report it looks like you initially processed your data set
>> using the "full" chip type. See below.
>>
>> On Fri, Nov 11, 2011 at 7:22 AM, wisekh6 <wise...@gmail.com> wrote:
>> > Dear all,
>>
>> > After processing Affymetrix GenomeWide SNP 6.0, I wanted to access
>> > 'chip effect data set' by using:
>> > cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
>> > XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6")
>>
>> > But, it failed, generating an error message: can't locate...
>>
>> Here you try to retrieve the data set as if it had been processed
>> using the standard (ie non "full") chip type, and apparently it was
>> not the case.
>>
>>
>>
>> > Using the following command successfully worked:
>> > cesN <- CnChipEffectSet$byName("AffyTestData",tags="ACC,ra,-XY,BPN,-
>> > XY,AVG,FLN,-XY", chipType="GenomeWideSNP_6,Full")
>>
>> This one works because what you ask to retrieve corresponds to what
>> you did initially.
>>
>> > The only difference is that the latter command used
>> > "GenomeWideSNP_6,Full" as chipType rather than "GenomeWideSNP_6."
>>
>> > Does anyone let me know why the former command failed to work?
>> > Originally, I believed that the former command would be correct.
>>
>> As explained above, both commands are "correct", but the first one
>> cannot retrieve what you ask because the corresponding processed data
>> set does not exist.
>>
>>
>>
>> > FYI: The corresponding annotation file is in the following directory:
>> > annotationData\chipTypes\GenomeWideSNP_6
>>
>> > Thank you.
>>
>> I hope this helps,
>>
>> Pierre
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> > --
>> > 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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>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>
> --
> 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
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
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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