[BioC] Analysis of many Flagged spots

[Davide Valentini]

Hi to all,

I've to deal with a dataset that has a huge amount of flagged as "bad" 
spots. My data are from peptide microarrays and the proportion of flags 
is around the 90% in each slide. Luckily I have a good set of samples 
(35 cases and 35 controls), but I'm not an expert with this kind of 
problem. Should I treat the flagged data as missing values and so try to 
impute new values instead the flagged "bad" spots ? I know the KNN 
imputation or the SVD imputation.
What is normally done with the spots flagged as "bad" (-100, following 
GenePix criteria + additional criteria) in cDNA experiments ?

Sorry if the question looks banal, but as I said I'm not an expert on 
this field. Any help is useful, also links regarding flagged data 
analysis...

Thanks in advance,

Davide


-- 
Davide Valentini
PhD - Biostatistician
Department of Medical Epidemiology and Biostatistic
Karolinska Institute
Box 281
SE-171 77 Stockholm
SWEDEN
Tel: +46-8-524 82294
Fax: +46-8-31  4975