[BioC] combining/merging several ExpressionSet objects from SCAN
Johnson, William Evan
wej at bu.edu
Sun Aug 11 02:01:29 CEST 2013
Steve,
Will you take a look at this thread and make any other suggestions.
Thanks!
Evan
On Aug 10, 2013, at 6:00 AM, <bioconductor-request at r-project.org>
wrote:
> Date: Fri, 9 Aug 2013 13:00:38 -0700
> From: "Tim Triche, Jr." <tim.triche at gmail.com>
> To: Juliet Hannah <juliet.hannah at gmail.com>
> Cc: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: Re: [BioC] combining/merging several ExpressionSet objects
> from SCAN
> Message-ID:
> <CAC+N9BXaZjiSyEaUduyZWB37XtT5LERTj3mPE1fCateTNW0x2w at mail.gmail.com>
> Content-Type: text/plain
>
> use saveRDS(foo, file='foo.rds') and then when you reload it with readRDS,
> the resulting object can have whatever name you like.
>
>
>
>
> On Fri, Aug 9, 2013 at 12:47 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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>>>>>
>>>>
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>>>>
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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>
>>>
>>
>>
>
>
> --
> *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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