DiffBind normalization returned NULL
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Entering edit mode
5 months ago
bertb ▴ 10

Hello,

I am trying to normalize some ChIPseq data in DiffBind, and having some difficulty with the command dba.normalize. When I try to examine the normalization methods and library size, I simply get NULL returned.

> B.DBcount
6 Samples, 1173 sites in matrix:
    ID Condition Treatment Replicate    Reads FRiP
1 wt1b        WT      none         1 16902874 0.20
2 mt1b        MT      none         1 14594474 0.13
3 wt2b        WT      none         2 16878697 0.22
4 mt2b        MT      none         2 14289354 0.15
5 wt3b        WT      none         3 18699283 0.24
6 mt3b        MT      none         3 15424246 0.20
> norm <- dba.normalize(B.DBcount, bRetrieve=TRUE)
> norm
NULL
> norm$norm.method
NULL

Any help greatly appreciated! Thanks

DiffBind dba.normalize normalization ChIPseq • 309 views
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2
Entering edit mode
5 months ago
Rory Stark ★ 1.6k

You can't normalize and retrieve the result in the same call to dba.normalize(). In order to retrieve information about how normalization has been computed, you need to normalize the data first.

You can get the default normalization as follows:

B.DBcount <- dba.normalize(B.DBcount)
norm <- dba.normalize(B.DBcount, bRetrieve=TRUE)
norm
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Entering edit mode

That makes sense - this worked.

Thank you!

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