SVA has just been updated, apparently, for use with sequencing data; see this preprint.
How to detect and correct batch effect in NGS expression data ?
2 answers
- Have a look at a PCA plot.
- Give the SVA package from Bioconductor a try.
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Ram
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Devon Ryan
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Devon Ryan
The ssva functionality looks particularly interesting.
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Devon Ryan
Is SVA is better than Combat?
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Ram
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Alastair Kerr
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Alastair Kerr
It sort of depends on your goals and circumstances. If you have known batch effects that and can use an expression-set as output, then combat would seem the better choice. If you need to known how many unknown batch effects you might have and appropriate weights for the various samples then sva is a better choice.
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Devon Ryan
edX course HarvardX: PH525x Data Analysis for Genomics week6 for removing batch effect https://courses.edx.org/courses/HarvardX/PH525x/1T2014/courseware/2273065cc0f649b69c1240a58f7ab080/
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Ram
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Ming Tommy Tang
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Ming Tommy Tang
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