[BioC] Quality checks / flagging

Gordon Smyth smyth at wehi.edu.au
Thu Sep 18 19:10:11 MEST 2003

At 05:52 PM 18/09/2003, Yves Bastide wrote:
>>>An even more elementary question (disclaimer: I am not a statistician): 
>>>how to use these weights to make limma ignore some lines?  I naively 
>>>tried with weights of 0 and 1, but it didn't work as expected.
>>Weights of 0 and 1 do have the effect of ignoring the log-ratios for 
>>spots with zero weight. I am not sure what you mean by "ignore some 
>>lines". Please explain further what you did and what you expected to 
>>happen which didn't.
>Oh.  I zero-weighted flagged spots and spots for unwanted genes.  This 
>resulted in about 600 genes to consider on each array, out of 4096.

In my honest opinion, throwing out almost all your data from a microarray 
experiment is crazy unless you have decided that there is something 
seriously wrong with the array. If you really want to do this, then please 
use normalizeWithinArrays with method="loess" rather than the default. 
You've thrown out almost all your data so there really isn't enough left to 
expect to be able to do normalization by print-tip groups.


>  Then, the result of normalizeWithinArrays is strange, the final coef vs. 
> lodds more so. (However, P-values and B are much better :) ).
>Same for weighting-out only flagged genes, keeping 'bout 1/3 of them. As 
>I'm just starting playing with statistic tools, I don't know what is 
>expected and what is clearly wrong.

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