[BioC] illumina --> limma?

[Sean Davis]

On 8/24/06 7:38 PM, "Mark Dunning" <md392 at cam.ac.uk> wrote:

> Hi Wolfgang,
> 
> Thanks for the advice about the logarithm transformation. I think the data
> in question here is the output from the Illumina software, in which case it
> will have already been background corrected at the individual bead level and
> summarised in a single value for each gene. Can the vsn transformation still
> be safely applied to this data?
>
> btw I would recommend using only the non-normalised output from the Illumina
> software if you plan to analyse on the log2 scale. All of the Illumina
> normalisation methods use a "background normalisation" step first which
> seems to create a lot of negative values. Illumina like to analyse all their
> data on the un-logged scale despite a very obvious relationship between the
> mean and variance. In fact, they take this relationship into account in
> their models for differential expression. If anyone is interested, the
> following paper discusses their methods:

Mark, 

Have you made any headway with Illumina regarding getting data that is
closer to "raw" but still useful?  We are getting the probe-level data
dumped from our (which I think is NOT background-subtracted, but correct me
if I am wrong), but these data do not conform to the usual Illumina output
(different unique ids for the probes), so I really haven't given much
thought to using them, particularly since I can't convince our collaborators
to make hacks of their scanner config file to get the dumps for all the data
we receive.

Sean