[BioC] Quality checks / flagging
Yves.Bastide at irisa.fr
Thu Sep 18 11:58:36 MEST 2003
Gordon Smyth wrote:
> 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
Yep, that's the conclusion I arrived to. My basic flawed methodology
was to find differentially expressed genes in one group, then re-read
the arrays for another group, lather, rince, repeat. Gee.
PS: one question on limma.R (1.2.1, 1.2.2)
toptable, line 511: does the else apply to the right if?
if(sort.by=="A") stop("Cannot sort by A-values as these
have not been given")
(and yes, I'm a Python user)
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