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22.6 years ago • updated 2.2 years ago
Gordon Smyth
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Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
by
James W. MacDonald
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Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do.
I would personally check to see if there is any…
Comment: Can NanoString data be analyzed using DESeq2?
by
James W. MacDonald
68k
You can always discard, although you can also retain them to check for unexpected differences.
Comment: DESeq2 on NanoString Data
by
Michael Love
43k
Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc.
It is close to SVA, we discuss both in the workflow…
Comment: DESeq2 on NanoString Data
by
thkapell
▴
10
Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…
Comment: Can NanoString data be analyzed using DESeq2?
by
thkapell
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Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…
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