[BioC] filtering

[J.delasHeras at ed.ac.uk]

Quoting Lev Soinov <lev_embl1 at yahoo.co.uk>:

>   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 at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
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