[flowStats] bug?
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selwyn quan ▴ 10
@selwyn-quan-3628
Last seen 7.2 years ago
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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@nishant-gopalakrishnan-3253
Last seen 7.2 years ago
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@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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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