[BioC] [flowStats] bug?

[Nishant Gopalakrishnan]

Hi Selwyn,

Thanks for pointing that out.  I have checked in changes to the devel
version of  flowCore and flowStats to fix this issue. It should now work
fine for flowFrames with/without the time channel.

Nishant


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of selwyn quan
Sent: Monday, August 17, 2009 11:15 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] [flowStats] bug?

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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