[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
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.
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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