[BioC] filtering

[J.delasHeras at ed.ac.uk]

Hi Lev,

I am not sure I follow you.
I know the raw data you were talking about was log-transformed. I'm  
not sure what you're trying to say now.

Jose


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

> Dear Jose,
>
>   I meant log trasformed raw data of course.
>   Sorry for any misunderstanding. The plots that I posted were on   
> the log2 scale.
>
>   Thank you,
>   Lev.
>
> J.delasHeras at ed.ac.uk wrote:
>   Quoting Lev Soinov :
>
>>
> [...]
>> Also, it is often assumed that log transformed raw signal is
>> roughly Normal.
>
> where do you get that idea?
>
> My raw signals are anything but normally distributed! In fact, they
> look a lot like yours.
> The *log ratios*, however...
>
> And the distribution depends a lot on the actual array and the actual
> experiment. I was recently looking at some yeast tiling arrays probed
> with the product of doing chromatin immunoprecipitation with an
> antibody against a protein that is present along the body of genes.
> Almost everywhere, in fact, given the gene density of yeast. In this
> particular case, the raw data looks entirely different to yours (and
> to the arrays I usually deal with). The log ratios, however...
>
> 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
> Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:   
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> ---------------------------------
>  Yahoo! Mail is the world's favourite email. Don't settle for less,   
> sign up for your freeaccount today.



-- 
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
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK