[BioC] combining/merging several ExpressionSet objects from SCAN

[Martin Morgan]

On 08/13/2013 04:24 PM, Tim Triche, Jr. wrote:
>> Tim: I thought combine() has binary.
>
> I was curious about this, so I went and looked.  It's binary in
> methods-eSet.R, or so it appears, but:
>
> library(GEOquery)
> gset <- getGEO('GSE40279')
> length(gset)
> ## [1] 3
> sapply(gset, ncol)
> ## GSE40279_series_matrix-1.txt.gz.Samples
> ##                                     255
> ## GSE40279_series_matrix-2.txt.gz.Samples
> ##                                     255
> ## GSE40279_series_matrix-3.txt.gz.Samples
> ##                                     146
> gset <- do.call(combine, gset)
> ## Error in as.vector(x, "character") :
> ##   cannot coerce type 'closure' to vector of type 'character'
> gset <- combine(gset[[1]], gset[[2]], gset[[3]])
> ## no problem
> ncol(gset)
> ## Samples
> ##    656
>
> The part that baffles me is that I don't see anywhere that combine() would
> recurse in the source!

It's the generic that does the magic

 > getGeneric("combine")
nonstandardGenericFunction for "combine" defined from package "BiocGenerics"

function (x, y, ...)
{
     if (length(list(...)) > 0L) {
         callGeneric(x, do.call(callGeneric, list(y, ...)))
     }
     else {
         standardGeneric("combine")
     }
}
<environment: 0x646ceb0>
Methods may be defined for arguments: x, y
Use  showMethods("combine")  for currently available ones.

>
>
>
> On Sat, Aug 10, 2013 at 5:43 PM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> Tim: I thought combine() has binary.
>>
>> Juliet: this often comes up.  You can do
>>    assign("NAME", object)
>> which is essentially equivalent to
>>    NAME <- object
>> Then you can also get the object by
>>    get("NAME")
>>
>> Kasper
>>
>>
>>
>> On Fri, Aug 9, 2013 at 3:47 PM, Juliet Hannah <juliet.hannah at gmail.com>wrote:
>>
>>> Thanks Tim.
>>>
>>> I'm trying this out and looks like I did not think this through. So let's
>>> say I have several CEL files.
>>>
>>> I am spreading this out over a cluster. So I have
>>>
>>> myFiles = ("cel1.CEL","cel2,CEL")
>>>
>>> # pick one file
>>>
>>> fileToNormalize = myFiles[fileIndex]
>>>
>>> # normalize this to create eset
>>>
>>> normalized = SCAN(fileToNormalize)
>>>
>>> # create unique output name to save
>>>
>>> outFileName <- paste(fileToNormalize,".Rdata",sep="")
>>>
>>> save(normalized,file=outFileName)
>>>
>>> My problem is now an R one, but related to this problem. "normalized" must
>>> be given a unique name so that when I load
>>> all the esets back in they have different names.
>>>
>>> Any suggestions?
>>>
>>>
>>>
>>>
>>> On Fri, Aug 9, 2013 at 3:27 PM, Tim Triche, Jr. <tim.triche at gmail.com
>>>> wrote:
>>>
>>>> qux <- combine(foo, bar, baz)
>>>>
>>>> if foo, bar, and baz are all ExpressionSets (or other eSets of suitable
>>>> mien) with the same fData rows and pData columns.
>>>>
>>>> I did this the other day for a huge GEO dataset that came as 3 separate
>>>> Esets off of getGEO.  (Then I turned it into a SummarizedExperiment, of
>>>> course)
>>>>
>>>>
>>>>
>>>> On Fri, Aug 9, 2013 at 12:22 PM, Juliet Hannah <juliet.hannah at gmail.com
>>>> wrote:
>>>>
>>>>> Thanks Ryan. I'll try this out. What if the esets are already
>>> generated.
>>>>> So
>>>>> I have a bunch laying
>>>>> around. I'll look into your answer more and see if I can apply it to
>>> this
>>>>> situation.
>>>>>
>>>>>
>>>>> On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson <rct at thompsonclan.org
>>>>>> wrote:
>>>>>
>>>>>>     celfiles <- list.files(pattern=".*\\.CEL$"**)
>>>>>
>>>>>>     scan.esets <- lapply(celfiles, SCAN)
>>>>>>     scan.eset <- Reduce(combine, scan.esets)
>>>>>>
>>>>>> I forget what package the "combine" function is from, but I assume
>>> it's
>>>>>> the same package that provides the ExpressionSet class.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Fri 09 Aug 2013 12:11:05 PM PDT, Juliet Hannah wrote:
>>>>>>
>>>>>>> All,
>>>>>>>
>>>>>>> SCAN outputs an ExpressionSet object for each CEL file. What is a
>>> nicer
>>>>>>> way
>>>>>>> to put them all into a matrix other than converting each one to a
>>>>> vector
>>>>>>> and then cbinding after each conversion?
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Juliet
>>>>>>>
>>>>>>>          [[alternative HTML version deleted]]
>>>>>>>
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>>>>>>
>>>>>
>>>>>          [[alternative HTML version deleted]]
>>>>>
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>>>>
>>>>
>>>>
>>>> --
>>>> *He that would live in peace and at ease, *
>>>> *Must not speak all he knows, nor judge all he sees.*
>>>> *
>>>> *
>>>> Benjamin Franklin, Poor Richard's Almanack<
>>> http://archive.org/details/poorrichardsalma00franrich>
>>>
>>>>
>>>
>>>          [[alternative HTML version deleted]]
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>>
>>
>
>


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