[BioC] combining/merging several ExpressionSet objects from SCAN

[Johnson, William Evan]

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]]