[BioC] What wrong with my data using LIMMA

[Gordon Smyth]

At 08:08 AM 6/09/2005, Adaikalavan Ramasamy wrote:
>Gordon, this is a good point that you raise. But can I ask you another,
>somewhat harder, question ?
>
>What should one do when the an arrays fail quality assessment. Do we
>simply omit it or can we possible correct for them. The decision to omit
>might be the obvious one but it seems a bit wasteful when the the
>proportion of arrays is large.
>
>I would be equally happy to hear from others on the list as well.
>
>Regards, Adai

In some cases poor quality arrays will  have to be dropped, but an 
alternative is to downweight the lower quality arrays using the 
arrayWeights() function in limma or array level standard errors from affyPLM.

Gordon