[BioC] lumiR error

Pan Du dupan at northwestern.edu
Mon Jan 18 16:17:16 CET 2010

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using outdated packages or data in the wrong format.


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

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