[BioC] Low Ratio values in LIMMA

[Nataliya Yeremenko]

Dear Greg

Thanks for your comment:
Detailed description and a number of problems are described in
my new BioC post with subject: Design question in LIMMA

As for data preporcessing  step I used ordinary:
RG <- backgroundCorrect(RG,method="minimum")
MA <-normalizeWithinArrays(RG, method="loess")
MA <- normalizeBetweenArrays(MA, method="Aquantile")

I didn't use weighting of the control spots (commercial Agilent 44K)
and didn't used anything flaged by Feature Extraction.
Maybe I have to?

I visualize the data afterwards and they look not bad.

I do understand that the data in topTable are in log2 scale,
but  the differences seem to me  to be really  small.
The problem may  come as well from the wrong design and contrasts created.
I hope this makes clear procedures I used.

Regards
Nataliya

Greg Finak wrote:

> Hi, Nataliya.
>
> This is very much dependent on how you normalize your data. It's  
> possible to "over normalize" and wipe out most of the variability in  
> your data. If you're certain that this isn't the case, then, no,   
> Limma doesn't generate shrunken estimates of the expression ratios,  
> only t-statistics. The expression ratios presented by limma will  
> either be log2, or a data dependent scale if you've used VSN to  
> normalize. Feel free to post more information about your  
> normalization / preprocessing / experimental design, that would help  
> to identify potential reasons, otherwise we're just speculating.
>
> Cheers,
>
>
> --------------------------------------------
> Greg Finak
> PhD Candidate
> McGill Center For Bioinformatics
>
> W: (514)398-7071 x09317
> emai: finak at mcb.mcgill.ca
> --------------------------------------------
>
> On 9-Nov-05, at 7:13 PM, Nataliya Yeremenko wrote:
>
>> Hello everybody
>>
>> After successful importing the data to the LIMMA,
>> I followed all steps and finally obtained "topTable".
>> (the data were 44K Agilent)
>> I'm surprised that my data set doesn't have anything with M-values  more
>> than 1.5.
>> I well understand that it depends on the experiment,
>> but is there some condensation of the Ratio during normalization and
>> other procedures?
>>
>> regards
>>
>> -- 
>> Dr. Nataliya Yeremenko
>>
>> Universiteit van Amsterdam
>> Faculty of Science
>> IBED/AMB (Aquatische Microbiologie)
>> Nieuwe Achtergracht 127
>> NL-1018WS Amsterdam
>> the Netherlands
>>
>> tel. + 31 20 5257089
>> fax  + 31 20 5257064
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>
>


-- 
Dr. Nataliya Yeremenko 

Universiteit van Amsterdam
Faculty of Science
IBED/AMB (Aquatische Microbiologie)
Nieuwe Achtergracht 127
NL-1018WS Amsterdam
the Netherlands

tel. + 31 20 5257089
fax  + 31 20 5257064