[BioC] normalising with bad slides

[James W. MacDonald]

Hi Andrew,

On 8/30/2010 3:12 AM, Andrew Einhorn wrote:
> I have a set of 15 human gene st arrays that I am normalising.  From
> analysis of the raw data, I can see that two of the slides are of very poor
> quality (signs of rna degradation, low pearson correlations etc).  If I do
> an rma normalisation and include these two slides, will they effect the
> normalisation of the other slides.  In other words, is it necessary to
> ignore these two slides in the rma step, or will including them make no
> difference.

It *should* have minimal repercussions if you include the two bad 
slides. The normalization relies on the median value for each probe, so 
your poor quality chips will not likely be used.

In addition, the model fitting process uses medians as well, so assuming 
that your poor quality chips return outlier values for each probeset, 
they won't be used for the model fit either.

Best,

Jim



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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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