search

wdl2459 / ConQuR

Batch effects removal for microbiome data via conditional quantile regression
GNU General Public License v3.0
27 stars 4 forks source link

easy bug fix - ConQuR_each should take in batchid #14

Open tommyfuu opened 1 year ago

tommyfuu commented 1 year ago

as mentioned in the title. it currently causes an error. can try to fix together on monday!

tommyfuu commented 1 year ago

seconding this again to add details as a bug fix - i can probably try to work on it as well. but here's the error:

Error in { : task 146 failed - "object 'batchid' not found"
Calls: run_methods -> ConQuR -> %do% -> <Anonymous>

What's causing it?

lines 166, 207 of ConQuR_help_functions.R calls batchid which is not defined in the function.

trx296554555 commented 1 year ago

Same question.

Error in { : task 1450 failed - "找不到对象'batchid'" Calls: remove_batch_effect -> ConQuR -> %do% -> <Anonymous> 此外: There were 50 or more warnings (use warnings() to see the first 50) 停止执行

The same data, when running in Rstudio on Windows, did not generate this error, but the error occurred when running on Linux CentOS 8.

wdl2459 commented 1 year ago

Thank you both for pointing out the issue! The bug has been fixed, and the updated software will be pushed soon. Also, we developed ConQuR_rel, which is designed for relative abundance (within each sample, the sum of all taxa's relative abundance is 1), as a complement to the original ConQuR paper. ConQuR_rel will also be pushed soon.