[BioC] Error, while using produceGEOSampleInfoTemplate

Aliaksei Holik salvador at bio.bsu.by
Wed Oct 3 15:59:19 CEST 2012

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 
 > 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"
[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,


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)

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United 
[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 
[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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