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Last seen 9.7 years ago
Hi,
Chapter 7 of the limma User's Guide introduces the concept of
filtering after normalization. I'm not entirely sure how this step
should be performed. Is this simply the removal of probes flagged as
poor quality by the scanner/quality assessment criteria? If so, should
all spots associated with this probe be removed across all replicates
or should it simply be the spot in question specific to that array?
The former approach would effectively remove the probe from the
experiment but the second would simply mean that the size of the
sample used to fit the linear model for that probe would be reduced by
one.
Of course, maybe neither of the above approaches are correct. If this
is so, could somebody provide some insight for this step. The user's
guide suggests, "one way is to keep probes that are expressed above
background on at least n arrays, where n is the smallest number of
replicates assigned to any of the treatment combinations." What does
this mean?
Thanks.
Matt
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