Question: rwehrens BatchCorrMetabolomics: doBC results in NA
0
gravatar for ab123
4 months ago by
ab12340
London
ab12340 wrote:

Hi folks,

Wondering if anyone could help:

I've formatted my data to resemble the example data so I'm not getting what should be wrong here.

Trying to use doBC but only getting a logical with NAs on return.

I checked that all the inputs were the same as the example data and there doesn't seem to be an issue.

Any ideas or someone with previously similar issues?

Thank you!

> M2c <- doBC(data[,2], ref.idx = ref.idx,
+             batch.idx = batch_labels$Batch, method = "rlm",
+             seq.idx = batch_labels$SeqNr)
> 
> M2c
 [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[38] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[75] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
ADD COMMENTlink written 4 months ago by ab12340

Finally solved this by taking a closer look at the raw code. Just in case someone has the same problem in the future: It was the minBsamp argument which requires a specified number of reference samples for each batch. If that number doesn't match or is not even across the dataset, the algorithm produces NA values.

ADD REPLYlink written 4 months ago by ab12340
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