Hi.
On Sun, Jun 26, 2011 at 6:00 PM, Dario Strbenac <dario.gar...@gmail.com> wrote:
> Hello,
>
> The append function works in a strange way because it modifies its
> first argument, as well as the result variable. Unusual for R, anyway.
Yes, most "aroma" objects are basically reference variables. This is
one of the reasons why the aroma framework can handle virtually
infinite number of arrays.
FYI, the underlying framework is the Object class of R.oo (which
basically is an extension to the environment class of R).
> It would be nice to document this behaviour.
Agree. Unfortunately, I/we have limited resources in document
everything. Keeping documentation up to date and consistent with
source code is very costly. The current strategy is therefore to keep
the Rd documentation at a minimum so it at least is correct. For the
aroma framework, the best "documentation" are the online vignettes
(and the source code of course).
This particular method - append() - is defined/implemented in the
R.filesets package. It's help pages in turn refers to the
appendFiles() method, which says that the value of the function is
"Returns (invisible) the appended data set (itself).". The term
"itself" is supposed to indicate that.
So, yes, your example below is expected.
/Henrik
> Notice in the example
> that both combined and celSet have been expanded to 12 elements.
>
> cdf <- AffymetrixCdfFile$byChipType("Hs_PromPR_v02")
>
> celSet <- AffymetrixCelSet$byName("H2A", cdf = cdf )
>> celSet
> AffymetrixCelSet:
> Name: H2A
> Tags:
> Path: rawData/H2A/Hs_PromPR_v02
> Platform: Affymetrix
> Chip type: Hs_PromPR_v02
> Number of arrays: 6
> Names: LNCaP_H2A_Input, LNCaP_H2A_IP1, LNCaP_H2A_IP2, ...,
> PrEC_H2A_IP2 [6]
> Time period: 2009-03-06 11:54:53 -- 2009-03-06 15:54:41
> Total file size: 269.16MB
> RAM: 0.01MB
>
> celSet2 <- AffymetrixCelSet$byName("H2AZ", cdf = cdf )
>> celSet2
> AffymetrixCelSet:
> Name: H2AZ
> Tags:
> Path: rawData/H2AZ/Hs_PromPR_v02
> Platform: Affymetrix
> Chip type: Hs_PromPR_v02
> Number of arrays: 6
> Names: LNCaP_H2A.Z_Input, LNCaP_H2A.Z_IP1, LNCaP_H2A.Z_IP2, ...,
> PrEC_H2A.Z_IP2 [6]
> Time period: 2009-03-06 13:38:03 -- 2009-03-06 16:17:27
> Total file size: 269.17MB
> RAM: 0.01MB
> combined <- append(celSet, celSet2)
>
>> combined
> AffymetrixCelSet:
> Name: H2A
> Tags:
> Path: rawData/H2A/Hs_PromPR_v02
> Platform: Affymetrix
> Chip type: Hs_PromPR_v02
> Number of arrays: 12
> Names: LNCaP_H2A_Input, LNCaP_H2A_IP1, LNCaP_H2A_IP2, ...,
> PrEC_H2A.Z_IP2 [12]
> Time period: 2009-03-06 11:54:53 -- 2009-03-06 16:17:27
> Total file size: 538.33MB
> RAM: 0.02MB
>>
>> celSet
> AffymetrixCelSet:
> Name: H2A
> Tags:
> Path: rawData/H2A/Hs_PromPR_v02
> Platform: Affymetrix
> Chip type: Hs_PromPR_v02
> Number of arrays: 12
> Names: LNCaP_H2A_Input, LNCaP_H2A_IP1, LNCaP_H2A_IP2, ...,
> PrEC_H2A.Z_IP2 [12]
> Time period: 2009-03-06 11:54:53 -- 2009-03-06 16:17:27
> Total file size: 538.33MB
> RAM: 0.02MB
>
> --
> 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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