[BioC] Lumi and Beadstudio 1.5.13

[Pan Du]

Hi Claudio,

Thanks for reporting the problem. I am not sure why it reported error when
retrieving a missing column in a data.frame, usually it should return NULL
instead of reporting error.

To avoid this, please set the parameter convertNuID as FALSE, e.g.,
 r <- lumiR(filenames, convertNuID=FALSE)

It should solve the problem. Tell me if the problem still exists.


Pan




On 9/5/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Thu,  4 Sep 2008 12:04:29 +0200
> From: "claudio\.is\@libero\.it" <claudio.is at libero.it>
> Subject: [BioC] Lumi and Beadstudio 1.5.13
> To: "bioconductor" <bioconductor at stat.math.ethz.ch>
> Message-ID: <K6O1BH$DE2008FC6621FDEFF2634E135B59A423 at libero.it>
> Content-Type: text/plain; charset=iso-8859-1
> 
> dear all,
> 
> I recently tried to reload some old data anlysis which encompasses Illumina
> data from beastudio 1.5.13.
> 
> Notably a chunck of code that previously work now does not any more.
> in particular:
> 
>> filenames <- "myData.txt"
>> 
>> r <- lumiR(filenames)
> Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") :
>   undefined columns selected
> 
> 
> looking in the man it seems that the package was updated to the new Illumina
> Bead Studio output.
> 
> looking in the ma I guessed to put inputAnnotation=FALSE. but still nothing.
> 
> r <- lumiR(filenames, inputAnnotation=FALSE)
> Error in `[.data.frame`(annotation, , "PROBE_SEQUENCE") :
>   undefined columns selected
> 
> Now, I dont have the new software. what can I do?
> 
> 
>> sessionInfo()
> R version 2.7.2 (2008-08-25)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L
> C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base     
> 
> other attached packages:
> [1] lumi_1.6.2           mgcv_1.4-1           affy_1.18.2
> [4] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1


------------------------------------------------------
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