Hi, continuing on my analysis of RNAi screens, I have scaled and normalized
my plates and am considering whether to perform a platewise variance
adjustment (dividing by MAD(sample wells) on a given plate).

When I do the calculation, I see that the standard deviation of the sample
signals decreases when I perform the variance adjustment. However, the
overall signal per plate (say as measured by the median) shifts
dramatically. The result can be seen in a plate well series plot at
http://rguha.net/varianceadjust.pdf where the upper plot is for the
normalized data and the lower plot is the variance adjusted version of the
normalized data.

My question is:

1. While the variance across the plates has decreased by this adjustment, is
there a good/reliable way to decide when to do it?
2. Why does the overall signal from each plate shift after the variance
adjutsment? Does the result of the variance adjustment indicate that the
overall signal on say plate 2 is lower than for plate 1? (Which is not
apparent when just looking at the normalized data)

Any pointers would be appreciated,

-- 
Rajarshi Guha

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