[BioC] Generating GEO submission files from beadarray summary data
Aliaksei Holik
salvador at bio.bsu.by
Fri Oct 5 10:58:55 CEST 2012
Dear Mark,
I'm not sure what level of demand is for such functionality for you to
go through the trouble of adding it, but I'd very much appreciate the
code you mentioned.
Many thanks,
Aliaksei.
On 05/10/2012 09:51, Mark Dunning wrote:
> Hi all,
>
> At the moment, there is no function in beadarray for creating a GEO
> submission file. However, if people feel it would be a useful
> addition, I'd be willing to add it to the next release.
>
> In the meantime, I think you might have to hack the existing code in
> lumi to work. I have some code that I wrote a while ago that I can
> send you. It seemed to work for my purposes.
>
> Mark
>
> On Fri, Oct 5, 2012 at 12:58 AM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
>> Hard to say, I don't use the beadarray package much these days, but the
>> functions that Lumi includes to generate a SOFT file and GEO submission all
>> assume that you will feed it a LumiBatch or MethyLumiM object to work from.
>> You might have more luck with Pan or Mike, so I am cc:'ing them and the
>> list.
>>
>> Best,
>>
>> --t
>>
>>
>> On Thu, Oct 4, 2012 at 4:52 PM, Aliaksei Holik <salvador at bio.bsu.by> wrote:
>>
>>> Dear Tim,
>>>
>>> Thanks for your clarifications. I am now trying to either convert existing
>>> beadarray generated data into LumiBatch or generate a GEO submittable file
>>> from it. But before I embark on a fun if time consuming mission of writing
>>> my own code, I would appreciate if you or anybody else could advise me if
>>> such functions are already available.
>>>
>>> Many thanks!
>>>
>>> Aliaksei.
>>>
>>> On 03/10/2012 15:56, Tim Triche, Jr. wrote:
>>>
>>>> yes, you need it to be a LumiBatch or other preprocessing-annotated
>>>> object in order for the information to be found
>>>>
>>>> ExpressionSetIllumina apparently doesn't contain that information. try
>>>> running traceback() after you get the error
>>>>
>>>>
>>>>
>>>> On Wed, Oct 3, 2012 at 6:59 AM, Aliaksei Holik <salvador at bio.bsu.by
>>>> <mailto:salvador at bio.bsu.by>> wrote:
>>>>
>>>> Apologies for re-posting this, but I'm concerned that the first
>>>> instance got lost. Never again, I promise :)
>>>>
>>>>
>>>> Dear Pan and fellow Biocondictors,
>>>>
>>>> I am trying to generate a file for submission to GEO database.
>>>> However, when trying to generate a Template File I'm confronted by
>>>> the following error:
>>>> > produceGEOSampleInfoTemplate(_**_normalised.data,
>>>> + lib.mapping=__**lumiMouseIDMapping, fileName="GEOTemplate.txt")
>>>> The input object should be an object of LumiBatch, MethyLumiM,
>>>> matrix or other ExpressionSet inherited class!
>>>> Error in templateContent[templateTitle == "Sample_data_processing"]
>>>> <- preprocessMethod :
>>>> object 'templateContent' not found
>>>>
>>>> The normalised.data file has been produced using beadarray package
>>>> and has the following class:
>>>> > class(normalised.data)
>>>> [1] "ExpressionSetIllumina"
>>>> attr(,"package")
>>>> [1] "beadarray"
>>>>
>>>> I understand, this would qualify it as an ExpressionSet inherited
>>>> class and I'm at loss, why it isn't recognised by
>>>> produceGEOSampleInfoTemplate.
>>>>
>>>> I wonder if I should re-code my ExpressionSet as some other class,
>>>> and how I might do that. Any help would be much appreciated,
>>>>
>>>>
>>>> Aliaksei.
>>>>
>>>> P.S. My sessionInfo output and lumi loading messages:
>>>>
>>>> > sessionInfo()
>>>> R version 2.15.0 (2012-03-30)
>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
>>>> Kingdom.1252
>>>> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
>>>> [5] LC_TIME=English_United Kingdom.1252
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] lumi_2.8.0 nleqslv_1.9.4 methylumi_2.2.0
>>>> BiocInstaller_1.4.7
>>>> [5] ggplot2_0.9.2.1 reshape2_1.2.1 scales_0.2.2
>>>> Biobase_2.16.0
>>>> [9] BiocGenerics_0.2.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> Error in x[["Version"]] : subscript out of bounds
>>>> In addition: Warning message:
>>>> In FUN(c("affy", "affyio", "annotate", "AnnotationDbi", "bigmemory",
>>>> :
>>>> DESCRIPTION file of package 'RSQLite' is missing or broken
>>>>
>>>> > library(lumi)
>>>> Loading required package: methylumi
>>>> Loading required package: nleqslv
>>>>
>>>> bigmemory >= 4.0 is a major revision since 3.1.2; please see package
>>>> biganalytics and http://www.bigmemory.org for more information.
>>>>
>>>> KernSmooth 2.23 loaded
>>>> Copyright M. P. Wand 1997-2009
>>>>
>>>> Attaching package: ‘lumi’
>>>>
>>>> The following object(s) are masked from ‘package:methylumi’:
>>>>
>>>> estimateM, getHistory
>>>>
>>>> Warning messages:
>>>> 1: replacing previous import ‘image’ when loading ‘graphics’
>>>> 2: package ‘nleqslv’ was built under R version 2.15.1
>>>> 3: replacing previous import ‘density’ when loading ‘stats’
>>>> 4: replacing previous import ‘residuals’ when loading ‘stats’
>>>>
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>>>>
>>>>
>>>> --
>>>> /A model is a lie that helps you see the truth./
>>>> /
>>>> /
>>>> Howard Skipper
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>>>>>
>>>>
>>>>
>>
>>
>> --
>> *A model is a lie that helps you see the truth.*
>> *
>> *
>> Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
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