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@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>

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