[BioC] backgroundCorrect offset value

[James W. MacDonald]

Hi Prasad,

On 8/26/2011 11:00 AM, Prasad Siddavatam wrote:
>
>
> Hello Users,
>
> I have a question regarding the usage of backgroundCorrect function in LIMMA.
>
> when I do the following with offset 50, I am getting 2900 differentially
> expressed genes
> RG.b<- backgroundCorrect(RG, method = "normexp", offset = 50);
>
> where as, when I do the following with offset 1,
> I am getting 1300 differentially expressed genes
> RG.b<- backgroundCorrect(RG, method = "normexp", offset = 1);
>
> Please advise which offset value to be used? Why is offset value making
> so much difference?

I can't advise you on the offset to use; that is up to you as the data 
analyst. But I can explain why you get more genes with a larger offset.

When you do a local background correction of your data, for the set of 
spots that are fairly dim (not much different from background 
intensity), the resulting ratios can become unstable because the 
numerators and/or denominators get small. This gives the characteristic 
spreading of the MA plot at low intensities after background correction.

An extreme example would be the instance where the R and G channels are 
nearly identical (say, 200 and 205), so the uncorrected ratio is close 
to 1. But if the Rb and Gb values are, say 190 and 185, then the 
background corrected ratio will be 2! Adding 50 to the R and G values 
before background correction will dampen the ratio to 0.86, which is 
likely closer to truth.

If you do MA plots before background correction and then after, both 
with and without adding the offset you will see what I mean.

Best,

Jim



>
> I am using this for TWO channel data, which is read by "genepix".
>
> Greatly appreciate your help.
>
> Prasad
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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