**0**wrote:

I am trying to run flowbin on my multi-tube flow set and got error message when trying to calculate medianFIDist.

tube.combined <- flowBin(tube.list=X.sample@tube.set,

bin.pars=X.sample@bin.pars,

control.tubes=X.sample@control.tubes,

expr.method='medianFIDist',

scale.expr=T)

Applying flowBin to Unnamed Flow Expr Set

Quantile normalising binning parameters across tubes

Binning using kmeans

Filtering sparse bins.

78 bins removed, containing a total of 69991 or 34 % of events (averaged across tubes).

**Calculating medianFIDist for all populations.
Error in if (res < 1) res <- 1 : missing value where TRUE/FALSE needed**

In addition: Warning message:

Quick-TRANSfer stage steps exceeded maximum (= 14099950)

Traceback and some googling (https://rdrr.io/bioc/flowBin/src/R/getBinExpr.R) into the function told me that medianFIDist is assuming the data has been log transformed.

This assumption is false. All my FCS parameters are still linear. I did not perform a transformation on them. It seems to me that this is a foolish assumption to make. What if I run the function on data that has been transformed with a biexponentialTransformation, would it still fail? What can be done to fix this?

#Distance function: difference of MFIs medianFIDist <- function(test, control) { if(is.null(control)) stop('NULL control frame -- no control tubes specified?') #Note: assumes log transform has been applied, so relinearises before subtracting res <- median(10^test) - median(10^control) if(res < 1) res <- 1 log(res,10) }

Thanks

Kelly

**30**• written 9 months ago by kelly.joanne.andrews •

**0**