Hi Jose,
   
  I filtered those probes that had less than 50% of good signals in at least one of the treatments. That was because I had four treatments, making several contrasts in LIMMA. I did it in order to make contrasts comparable. So, each contrast (pair of treatments) contained the same set of probes. In your terminology I filtered on one channel, keeping only signals detectable on ALL arrays.
  The data shown in the plots are for just one of the arrays.
   
  My question was about whether such filtering would affect differential expression analysis if done before normalisation. Or it really does not matter when you filter before or after normalization step. Does this lead to anything undesirable or wrong, apart from loosing some genes that were "undetectable" in one treatment but "detectable" in some other treatments?
   
  Thank you,
  Lev.
   
   
  J.delasHeras@ed.ac.uk wrote:
  Quoting Lev Soinov :

> Dear List,
> I have posted a similar question before, but would like to ask you again
> about filtering strategies. I have some AB1700 data and filter on signal to
> noise ratios before normalization. The rationale is to get rid of badly
> measured signals before actual processing of the data. Two jpg 
> histograms of
> log2 signal distributions, before (raw.jpg) and after (filtered.jpg)
> filtering, can be seen in this location:
> http://tmgarden.cloud.prohosting.com/images/
> Could you please have a look at the distributions and comment on whether
> this is correct to filter before normalization as this changes the 
> distribution of
> signals a lot?
> Thank you very much for your help.
> Lev.

Hi Lev,

Not sure what's the problem here. Your data has a large number of very 
low intensity points, and you removed them. The filtered histogram 
looks then exactly like the raw one, minus the low intensity stuff 
(the large peak on the left). That looks normal.

I often do something similar, but I only remove the spots/probes that 
have low intensity in BOTH channels (if 2-colour hybs, if 1-colour 
then check on both samples that you are comparing), on ALL the 
relevant arrays. You seem to have filtered here only on one channel?

Jose


-- 
Dr. Jose I. de las Heras Email: J.delasHeras@ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK

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