[BioC] ChIP on Chip normalization

[Sean Davis]

On May 25, 2005, at 10:06 AM, Wolfgang Huber wrote:

>
> Hi Ido,
>
>> has anybody experience with Chromatin IP on Chip normalizations?
>> We use an oligo tiling array as well as a ~500bp DNA fragments 
>> spotted array (which is my priority currently). Are there special 
>> normalization procedures in some of the packages?
>> I couldn't find any of those yet.
>
> Normalization always needs to be adapted to the particular platform,
> quality issues etc. of the arrays at hand, but why do you think you 
> need
> a special normalization procedure for ChIP compared to RNA 
> hybridization?

In data we have looked at, the centrality paramater (whatever that is) 
is often not correct, as chIPchip data is effectively one-sided.  This, 
of course, depends on the experiment (high enrichment leads to a skewed 
distribuiton of ratios).  In any case, normalization will affect any 
downstream analyses you perform, so you need to understand how the 
normalization you choose might impact your ability to see "positive" 
probes.

Sean