[BioC] Error, while using produceGEOSampleInfoTemplate

[Aliaksei Holik]

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
> <http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>