[BioC] backgroundCorrect offset value

Wei Shi shi at wehi.EDU.AU
Mon Aug 29 01:15:48 CEST 2011

Dear Prasad,

The offset added to the data is used to achieve a good balance between precision and bias for the data analysis. The larger offset will give rise to higher precision (smaller variation between replicates), but it will yield larger bias as well (e.g. dampened fold changes). The paper below gives a systematic evaluation on the impact of using different offsets  on the precision, bias and false discovery rate for the Illumina BeadChip data. But it should be useful for other platforms as well.



On Aug 27, 2011, at 6:30 AM, Prasad Siddavatam wrote:

> Hi Jim,
> Thank you very much for you explanation. Now I can understand the reason. 
> But when you said its up to the analyst to decide on the offset value.
> Is this statement based on the number of genes I am 
> expecting (to be differentially expressed) or on some other criteria.
> Its is very critical because I am using several types of 
> arrays (agilent, cDNAs)
> Appreciate your help.
> Prasad
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