On Thu, Nov 17, 2011 at 11:06 AM, Kai <wangz...@gmail.com> wrote:
> Hi Henrik,
>
> Thank you. This is very useful. When I generate a CnChipEffectSet and
> convert it into an AromaUnitTotalCnBinarySet using the
> exportTotalAndFracB() function, does it matter how I have set the
> "mergeStrands" and "combineAlleles" when doing the probe summarization
> using "AvgCnPlm"?
No, exportTotalAndFracB() will automagically write TCN or TCN & BAF,
depending on what the object contains ("combineAlleles").
Honestly, I don't know what will happen if you use mergeStrands=FALSE.
/Henrik
>
> Thanks again.
>
> Best,
> Kai
>
> On Nov 16, 5:09 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi.
>>
>> On Wed, Nov 16, 2011 at 12:06 PM, Kai <wangz...@gmail.com> wrote:
>> > Hi Henrik,
>>
>> > For GWS6 data it seems to me that they can be processed to generate
>> > either an "AromaUnitTotalCnBinarySet" or a "CnChipEffectSet". For
>> > example, codes in your vignette "Estimation of total copy numbers
>> > using the CRMA v2 method" will produce a "CnChipEffectSet", whereas
>> > when one uses the "doCRMAv2" wrapper function it will produce an
>> > "AromaUnitTotalCnBinarySet".
>>
>> See how-to page 'Export total copy numbers and allele B fractions as
>> aroma binary data files':
>>
>> http://aroma-project.org/howtos/exportTotalAndFracB
>>
>> for creating/exporting a CnChipEffectSet (a special case of
>> SnpChipEffectSet) to an AromaUnitTotalCnBinarySet.
>>
>> That is actually what is done in the last step of doCRMAv2(), cf.
>> print(doCRMAv2.AffymetrixCelSet).
>>
>> An AromaUnitTotalCnBinarySet data set can hold locus-specific total CN
>> estimates from any type of CN technology, e.g. Affymetrix, Illumina
>> and Agilent. A CnChipEffectSet data set is customized for Affymetrix
>> only. In the beginning (of the aroma framework), there we only dealt
>> with Affymetrix so CnChipEffectSet was natural but in order to bring
>> in other technologies to we came up with the technology-independent
>> AromaUnitTotalCnBinarySet format.
>>
>> (Maybe we should update those explicit CN vignettes to always do
>> exportTotalAndFracB() at the end.
>>
>>
>>
>> > My question is whether these two data types are interchangeable? They
>> > don't seem able to be combined in downstream analysis such as
>> > CbsModel. The thing is that we processed the HAPMAP reference samples
>> > using "doCRMAv2" which produced an "AromaUnitTotalCnBinarySet"; and
>> > recently we processed another dataset following the example in "http://
>> >www.aroma-project.org/node/117" which produced a "CnChipEffectSet".
>> > However when we loaded both of them and tried to create a CbsModel
>> > using the pooled HAPMAP as reference, it failed.
>>
>> I haven't tried to mix the two types and I didn't think of that use
>> case when extending the downstream methods to support that, so it may
>> not work. What is the error you get? Either way, now you know how to
>> export to AromaUnitTotalCnBinarySet, so you should be fine.
>>
>>
>>
>> > Is there a way to convert the one object into the other?
>>
>> As above. There is no way implemented for going from an
>> AromaUnitTotalCnBinarySet to a CnChipEffectSet.
>>
>> > Or do we have
>> > to reprocess one dataset to generate the same type of object as the
>> > other?
>>
>> So, the answer is no.
>>
>> Hope this helps
>>
>> /Henrik
>>
>>
>>
>> > Thanks very much for your help.
>>
>> > Best,
>> > Kai
>>
>> > --
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>> > 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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--
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