voom with quality weights after RUV correction
1
0
Entering edit mode
@14ef1b09
Last seen 3 days ago
Egypt

Is it recommended to use voomWithQualityWeights() instead of conventional voom() when the data was already subjected to RUVg correction?

RUVSeq limma DifferentialExpression • 207 views
ADD COMMENT
2
Entering edit mode
@gordon-smyth
Last seen 45 minutes ago
WEHI, Melbourne, Australia

Applying RUV correction can sometimes clean up a dataset so well that quality weights are no longer required. In general though, the decision to batch correct and the decision to use quality weights are made separately. There is no general rule.

RUV is designed to correct for batch effects in the linear model. It is not designed to correct for differential variability associated with quality weights, so you should not necessarily assume that it avoids the need for quality weights.

ADD COMMENT
0
Entering edit mode

Is there a diagnostic plot that can help in making a decision?

ADD REPLY
2
Entering edit mode

The usual plotMDS() plot helps identify outliers and unequal variabilities.

ADD REPLY

Login before adding your answer.

Traffic: 576 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6