[Bioc-devel] Subsetting affybatch and exprset objects

[A.J. Rossini]

Would it be worth distinguishing between probesets and probes?  i.e. 

afbatch[ ]  indexing genes (and hence probesets) rather than probes?

(and I can't recall what [[ is indexing, but perhaps probes if it
isn't?)

(don't shoot me if I'm being stupid, I still havn't had coffee this
morning). 

best,
-tony



"Rafael A. Irizarry" <ririzarr at jhsph.edu> writes:

> the problem is th if you subset eset by the first dimension then you 
> loose the position structure, and as a consequence the locations of pms
> and mms held in the cdfenv are no longer meaningful. if there are any 
> suggestions on what eset[i,] should return id be happy to consider them.
>
> On Tue, 13 Apr 2004, Crispin Miller wrote:
>
>> Hi,
>> Apologies if I should have sent this to the main bioconductor list...
>> and tell me if you'd have preferred it there! ;-)
>> 
>> I've noticed an issue with subsetting ExprSet and AffyBatch objects -
>> and wondered what what peoples' thoughts were:
>> If I do a subsetting operation of an exprSet with 6 chips in, I get
>> this:
>> 
>> > eset.mas[1,]
>> Expression Set (exprSet) with 
>> 
>>    1 genes
>>    6 samples
>> 
>> > eset.mas[,1]
>> ...
>>    22283 genes
>>   1 samples
>> 
>> 
>> However, if I do the same with AffyBatch I get this:
>> 
>> > eset[1,]
>> AffyBatch object
>> ...
>> Number of samples=1
>> Number of genes=22283
>> 
>> >eset[,1]
>> AffyBatch object
>> Number of samples=6
>> Number of genes=22283
>> 
>> 
>> Soooo, to subset and exprSet by chip I have to type eset[,x], but for an
>> AffyBatch I must type: eset[x,], which is particularly confusing since
>> AffyBatch is a subtype of exprSet... Would it be possible/a good idea,
>> to make these two incantations the same for both classes?
>> 
>> Crispin
>>  
>> --------------------------------------------------------
>> 
>>  
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>
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-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
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