Question

DiffBind issue with edgeR$bTagwise and DESeq2$fitType

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jason.kost • 0

@74d92117

Last seen 8 months ago

United States

Noticed a discrepancy in config file parameter names.

In all documentation, the DBA$config$edgeR$bTagwise and DBA$config$DESeq2$fitType parameters are structured as written here. However, in the actual DBA object they are stored as DBA$config$edgeR.bTagwise and DBA$config$DESeq2.fitType

This causes problems when trying to run an analysis on a DBA object resulting in the following error:

"Analyze error: Error in pv$config$DESeq2$fitType: $ operator is invalid for atomic vectors"

I think this may only occur if the values are explicitly set in an external config, and a workaround seems to be to just manually set the correct parameter using the "." version's value.

Config DiffBind Error • 614 views

ADD COMMENT • link updated 9 months ago by Rory Stark ★ 5.2k • written 9 months ago by jason.kost • 0

score 0 · Answer 1 · 2023-07-26

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Rory Stark ★ 5.2k

@rory-stark-5741

Last seen 15 days ago

Cambridge, UK

There appears to be some ambiguity regarding using a config file to specify the configuration parameters. Currently, you are unable to use an external file to set nested configuration parameters, you can't use this method to set the $edgeR$bTagwise or $DESeq2$fitType parameters. You will need to set them manually, either in the call to dba() or after that call by explicitly setting $config$edgeR$bTagwise etc.

The substitution of '.' for '$' is an artefact of this limitation, and setting the config using a '.' will not work (it will not change the parameter). It must be specified as a nested list using '$'.

ADD COMMENT • link 9 months ago Rory Stark ★ 5.2k

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Just to clarify, when I mentioned manually setting the parameter, I meant an assignment within R such as:

sample_data$config$DESeq2$fitType <- sample_data$config$DESeq2.fitType

Not trying to use the "." form within the config.

ADD REPLY • link 9 months ago jason.kost • 0

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That should work, does it? If not, can you a) include the package versions being used (sessionInfo()) and more of your script so I can see how you are getting the error? I can't reproduce it as you've described it:

data(tamoxifen_counts)
dba.show(dba.analyze(tamoxifen),
         bContrasts=TRUE)
tamoxifen$config$DESeq2$fitType <- "mean"
dba.show(dba.analyze(tamoxifen),
         bContrasts=TRUE)

ADD REPLY • link 9 months ago Rory Stark ★ 5.2k