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wdl2459 / ConQuR

Batch effects removal for microbiome data via conditional quantile regression
GNU General Public License v3.0
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Run ConQuR without covariates #3

Closed andrewmaltezthomas closed 1 year ago

andrewmaltezthomas commented 1 year ago

Hi ConQuR developers,

I was wondering if there was a way to run the ConQuR() command without including any covariates, so just the batch. I tried using NULL, which returned an error:

Error in data.frame(covariates, batchid) : arguments imply differing number of rows: 0, 147

And I also tried using a vector with the batchIDs, which returned an identical count matrix to the original.

Thanks in advance.

tommyfuu commented 1 year ago

ran into the same issue, agree that this is probably a feature that needs to be added.

one thing i notice though is that the resultant dataframe from ConQuR is not that different from the original dataframe in general. I tried running ConQuR on a dataframe with covariates, as well as a dataframe without covariates where I used batchIDs as the placeholder covariate. looked pretty carefully and did notice subtle differences between the resultant dataframe and the input.

That might be worth double-checking?

wdl2459 commented 1 year ago

Thank you for the question! To use ConQuR without covariates, please make simple_match=T and keep covariates=NULL. Please let me know whether it works.

tommyfuu commented 1 year ago

that worked like a charm for me! thank you so much!

andrewmaltezthomas commented 1 year ago

Also worked for me. Thanks!