[BioC] Generating GEO submission files from beadarray summary data
Mark Dunning
mark.dunning at gmail.com
Fri Oct 5 10:51:13 CEST 2012
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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