[BioC] BeadExplorer error

[Martin Morgan]

Hi Alice --

It's a pretty good error! how can row.names(x) have a length different
from 1:length(x)? The answer is...

> x <- character(0)
> data.frame(1:length(x), row.names=x)
Error in data.frame(1:length(x), row.names = x) : 
  row names supplied are of the wrong length

because length(x) is 0 and 1:0 is c(1,0). So my guess is that the
sample names are not being read correctly from
Sample_Probe_Profile.csv. The use of widgets makes it difficult to
track down further or make a reproducible example, though traceback()
(and options(error=recover), for the enthusiastic) might be helpful.

Does that point in the right direction?

Martin

"Johnstone, Alice" <Alice.Johnstone at esr.cri.nz> writes:

> Hi
> I have been trying to get BeadExplorer to work with my Illumina data,
> but I get the following error when using either the txt or csv files:
>
>> data<-beadAnalysis()
> Read c:/R/Illumina/Sample_Probe_Profile.csv
> Error in data.frame(sample = 1:length(sampleNames), row.names =
> sampleNames) : 
>   row names supplied are of the wrong length
> In addition: Warning message:
> read.phenoData is deprecated, use read.AnnotatedDataFrame instead 
>
>
> I do note that this error has been posted on here before, but I haven't
> seen a resolution for it, can anyone help me here?
>
> Cheers,
> Alice
>
>> sessionInfo()
> R version 2.6.0 (2007-10-03) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
> [1] tcltk     tools     stats     graphics  grDevices utils     datasets
>
> [8] methods   base     
>
> other attached packages:
>  [1] BeadExplorer_1.4.0   tkWidgets_1.16.0     DynDoc_1.16.0       
>  [4] R2HTML_1.58          widgetTools_1.14.0   limma_2.12.0        
>  [7] lumiRatV1_1.3.1      lumi_1.4.0           annotate_1.16.0     
> [10] xtable_1.5-2         AnnotationDbi_1.0.5  RSQLite_0.6-3       
> [13] DBI_0.2-4            mgcv_1.3-28          affy_1.16.0         
> [16] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.1      
>
>
>
>
>
>
> P Think before you print
> This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed.
> If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Computational Biology Shared Resource Director
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (208) 667-2793