[BioC] lumiR error

[Pan Du]

Hi Paul

Please provide more detailed information, or else we cannot help you.
For example, please send me the returns of sessionInfo() and also the top
twenty lines of your data. I want to know whether it is because you are
using outdated packages or data in the wrong format.
Thanks!

Pan


On 1/16/10 5:24 PM, "gilbert feng" <g-feng at northwestern.edu> wrote:

> From: Paul Sanfilippo <prseye at gmail.com>
> Date: Sun, 17 Jan 2010 10:16:41 +1100
> To: <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] lumiR error
> 
> Dear List,
> 
> I'm new to microarray analysis, so go easy.  When I try to import some
> methylation data using lumiR, I receive the following error:
> 
>> meth<-lumiR("~/desktop/meth_sample.txt")
> Error in gregexpr("\t", dataLine1) : invalid 'text' argument
> 
> If I specify "sep":
> 
>> meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
> Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
>    subscript out of bounds
> 
> Does anyone know what might be causing the problem? Can lumiR handle
> this type of data where headers from BeadStudio are "..._Beta" instead
> of "..._Signal", etc
> 
> Thank you,
> 
> Paul Sanfilippo


--
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu