[BioC] help with lumiB

Pan Du dupan at northwestern.edu
Thu Oct 23 17:45:35 CEST 2008

Hi Leon,

I guess the problem was caused by the mismatch between the column names of
control probe data and expression data. Can you send me the return of
sessionInfo() and the code of adding control data to the LumiBatch object?
It will be helpful for me to find the problem. Thanks!


On 10/23/08 1:53 AM, "Leon Peshkin" <pesha at hms.harvard.edu> wrote:

> Dear Pan,
>     I was wondering if you could help me resolve the issue with lumi
> package,
> I am able to load Illumina data with lumiR, but then when I try
> background adjustment
> it fails:
>   A0 <- lumiR("killme.txt", convertNuID =FALSE, inputAnnotation =FALSE)
>> B0 <- lumiB(A0,method='bgAdjust')
> Error in `[.data.frame`(control, , sampleNames(lumiBatch)) :
>    undefined columns selected
> -Leon
> Dr. Leon Peshkin, Senior Research Scientist
> Systems Biology Dept.,    Longwood Av. 200
> Harvard Medical School, Boston, MA 02115
> tel: (617) 432-5483

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