On Tue, Nov 4, 2008 at 6:04 AM, John Lande <john.lande77@gmail.com> wrote:

> dear all,
>
> I am using lumi to normalize raw Illumina Data, but when I run the script,
> I
> retrive this error. can you help me?
>
> library(lumi)
>
> r=lumiR("gene_expression.txt")
>
> b=lumiB(r, method="bgAdjust")
>
> Perform bgAdjust background correction ...
> There is no control probe information in the LumiBatch object!
> No background adjustment will be performed.
>

Hi, John.  The lumi package needs control probe information to do background
adjustment.  It appears that your gene_expression.txt does not include the
control probes.  Also, I think this is just a warning, so you can probably
proceed with your analysis either way.  Finally, when posting to the list,
remember to include sessionInfo().

Sean

	[[alternative HTML version deleted]]

