[BioC] Error, while using produceGEOSampleInfoTemplate

Aliaksei Holik salvador at bio.bsu.by
Fri Sep 28 10:53:48 CEST 2012

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.

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 
[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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