Error in .checkedCall : subset indices out of range [closed]

Question

After normalization the way it is described here:

https://bioconductor.org/packages/3.7/bioc/vignettes/scran/inst/doc/scran.html

Using quickCluster() function and running computeSumFactors() I am trying to run calculateQCMetrics() the way it is described here:

https://f1000research.com/articles/5-2122/v2

sce <- calculateQCMetrics(sce, feature_controls=list(Mt=is.mito))

And I am getting an error:

Error in .checkedCall(cxx_colsum_subset, exprs_mat, is_feature_control) : subset indices out of range

Does anybody know how to correct it? What is going wrong here?

Answer 1

Just posted the question and found out why the error was happening. I had two datasets: raw, and filtered one with half of the rows as raw. I did normalization on the filtered one. Then I calculated is.mito using the unfiltered, raw dataset. So, it produced indexes that were outside of the range of the dataset.