Closed FMKerckhof closed 7 years ago
It is unclear to me how flowClean adjusts the volume measured based on the events removed? Removing spurious and erroneous measurements is a good thing for the diversity assessment but will bias the counts. I'll try to evaluate it on the test data set and try to incorporate it into the Diversity_rf
and beta_div_fcm
functions as an additional option.
if you'd need to evaluate/validate it with test data, say a defined concentration of peak beads, I could create the required FCS files with the FACSVerse or the C6
I've implemented the flowClean
function in the Diversity_rf
function and tested in on the test data (flowData
) but it did not detect any outliers. Will update wiki.
Wiki is updated for alpha div. Will update beta div function to offer the same functionality.
Have adjusted wiki - so everything should be good to go.
However, for sure with the latest release, the flowAI bioconductor package is probably the better option.
Recently, we saw with the Accuri that in high-throuphut experiments there could occur missed issues on stability of the data. Could we implement a standardized check? We already (briefly) evaluated flowClean (http://bioconductor.org/packages/release/bioc/html/flowClean.html), however it appears to be quite slow.
Suggestions: