[BioC] [flowStats] bug?

selwyn quan selwynq at stanford.edu
Mon Aug 17 20:14:58 CEST 2009


Am testing the probability binning function in the flowStats package but 
am given the following error message for this command:

proBin(f1[[1]], 200)

Error in xx[[1]] : this S4 class is not subsettable
Error in exprs(xx[[1]]) :
   error in evaluating the argument 'object' in selecting a method for 
function 'exprs'

A traceback gives:

3: exprs(xx[[1]])
2: flowCore:::findTimeChannel(m, strict = FALSE)
1: proBin(f1[[1]], 200)

The same command works for the GvHD test data set. I suspect the error 
occurs because there is no Time channel in my FlowSet. Looking at the 
following code the function seems to expect a Time Channel the 
flowSet. Is this expected behaviour??

> flowStats:::proBin
function (m, minEvents)
{
     timeCol <- flowCore:::findTimeChannel(m, strict = FALSE)
     colNames <- colnames(m)
     m <- exprs(m)[, colNames[!(colNames == timeCol)]]


Thanks,
Selwyn



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