[BioC] help with lumi

[Pan Du]

Hi Katie

The inputted annotation information is kept in the featureData slot. You can
retrieve it using following command:

 annotation = pData(featureData(x.lumi)) # suppose x.lumi is the LumiBatch
object keeping the data

As for doing multiple comparison at the same time using limma, yes you can
easily do it. But I suggest you read the tutorial of limma package. There
are lots of good examples to follow.


Pan


On 5/21/10 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 21
> Date: Thu, 20 May 2010 14:25:09 +0100
> From: "Taylor, Katie" <kt70 at leicester.ac.uk>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] help with lumi
> Message-ID:
> <413DBF04CB18DC45AEC6B64AEA6F9B60304D72975D at EXC-MBX1.cfs.le.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi,
> 
> I have just tried to load illumina microarray data into lumi and I added
> loadAnnotaion=TRUE. However, when I output the data to an .txt document, only
> the nuIDs are there and the annotation has gone. Does anyone know what i've
> done wrong?
> 
> Also, I have 24 samples, with 6 groups. How do I perform comparisons between
> the groups using limma? Can I do all of the comparisons at once, producing
> different documents for each or is it better to do each comparison
> individually? I would appreciate your comments.
> 
> I have copied the session info and R output for lumi below:
>