Diffbind batch effect blocking error
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rm1238 • 0
@rm1238-19204
Last seen 2.2 years ago

Hello Rory,

I am experiencing trouble trying to perform a dba with blocking factor (replicate in my case). My current dba object looks like this, and to my eyes, it has the correct format, indicating the Replicate metadata in the corresponding column

Escapeall ID Condition Treatment Replicate Caller Intervals FRiP 1 CtrlD81 Ctrl 0d 1 counts 127618 0.30 2 CtrlD82 Ctrl 0d 2 counts 127618 0.38 7 TreatD81 Treat 8d 1 counts 127618 0.36 8 TreatD8_2 Treat 8d 2 counts 127618 0.36

However, once I try to perform the analysis using the blocking factor, the following error appears:

Escapeallblock <- dba.analyze(Escapeall,block=DBAREPLICATE) Error in dba.analyze(Escapeall, block = DBAREPLICATE) : unused argument (block = DBA_REPLICATE)

I am failing to understand where the error is coming from, as the Replicate column is present in the sample sheet.

I am using R studio 1.2.1335 on a Mac OS 10.14.6

Thank you very much for your help,

Ricardo

Diffbind ATAC batch correction blocking factor • 321 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 17 days ago
CRUK, Cambridge, UK

block is not a parameter to dba.analyze(). If you want to do a blocking contrast, you need to add it explicitly using dba.contrast().

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Thanks a lot for the reply.

Cheers,

Ricardo

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Thanks a lot for the reply.

Cheers,

Ricardo

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