[BioC] dealing with negative values in illumina

[Simon Anders]

Hi Prasad

On 03/23/2011 06:28 AM, Prasad Siddavatam wrote:
> I am reprocessing a previously processed dataset from NCBI GEO. This is
a
> Illumina microarray chip. The data provided at GEO is either normalized
with
> negative probe values or unnormalized data without control spot
information.
>
> If I avoid the probes with the negative values (can't transfer to logs)
that
> leaves only 9500 out of 22000 probes?
>
> Can anybody please suggest how to approach this problem?

You should use the log transform only on florescence intensities or on 
ratios of these, anyway -- for other kind of data, it makes no sense. 
Raw florescence intensities typically have values between 0 and 2^16-1 = 
65535. If there are negative numbers among your data, you are looking at 
something else, and you shouldn't proceed before understanding that.

Maybe your data is already log transformed? If they log transformed 
ratios, you will get negative values whenever the ratio is smaller than 
1. If you log transform this a second time, you won't get anywhere.

   Simon