[BioC] BeadExplorer error

[Johnstone, Alice]

Using traceback give the following:

> traceback()
5: stop("row names supplied are of the wrong length")
4: data.frame(sample = 1:length(sampleNames), row.names = sampleNames)
3: read.phenoData(sampleNames = colnames(signal), widget = FALSE)
2: readBead(datafile, version = "Two")
1: beadAnalysis()

It can be run without the widget by instead using:

>Data<-readBead("Sample_Probe_Profile.csv")

Looking at this I think the "wrong length" error, when using the txt
file is coming from the "skip" argument in the read command as the txt
file from version 2 has no header rows to skip.  The version "One" reads
the csv format.. But trying this I then get an error

> data<-readBead("Sample_Probe_Profile.csv",version="One")
Read Sample_Probe_Profile.csv
Error in read.table(file = file, header = header, sep = sep, quote =
quote,  : 
  duplicate 'row.names' are not allowed

Enter a frame number, or 0 to exit   

1: readBead("Sample_Probe_Profile.csv", version = "One")
2: read.delim(filenames[1], skip = 7, sep = ",", row.names = 1)
3: read.table(file = file, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.cha


But my data comes from a Illumina Inc. BeadStudio version 2.3.41 so this
doesn't seem like the right way to go about it.  Does the row.names=1
refer to the first column?  As there are a few target Ids (the first
column) that have two probes so more than one row..


-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Thursday, 18 October 2007 5:32 p.m.
To: Johnstone, Alice
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] BeadExplorer error

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      
>
>
>
>
>
>
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--
Martin Morgan
Computational Biology Shared Resource Director Fred Hutchinson Cancer
Research Center 1100 Fairview Ave. N.
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