User: Greg Finak

gravatar for Greg Finak
Greg Finak150
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Posts by Greg Finak

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Answer: A: How are autofluorescence values used in the spillover/compensate functions?
... From looking at the code, which you can see for yourself by typing: getMethods(spillover) it seems autofluorescence for each channel is subtracted from the columns of the spillover matrix prior to re-normalizing it. I believe this follows the procedure described in the reference. From your descrip ...
written 2.7 years ago by Greg Finak150
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Comment: C: flowClust with prior: "randomStart>0 has no effect when using a prior"
... Thanks,  Turns out there was a bug in the code throwing the warning unnecessarily. I've pushed a fix, and it should appear some time tomorrow. Now setting randomStart=FALSE or 0 should suppress the warning properly. Greg ...
written 2.8 years ago by Greg Finak150
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Answer: A: flowClust with prior: "randomStart>0 has no effect when using a prior"
... Set randomStart=FALSE to eliminate this warning.   ...
written 2.8 years ago by Greg Finak150
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Comment: C: read.flowSet fails but read.FCS works
... There is a column.pattern argument that you could pass to read.flowSet, which is a regular expression specifying which markers to keep. See ?read.FCS for details. Best Greg ...
written 2.9 years ago by Greg Finak150
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Answer: A: read.flowSet fails but read.FCS works
... A couple of things to try: A flowSet must be composed of FCS files that have the same markers and the same number of channels in the same order. Is this the case for your data? The error you get is a but cryptic but that's what it's hinting at to me, and is a reasonable place to start checking. Can ...
written 2.9 years ago by Greg Finak150
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Answer: A: openCyto: Using combination gates (boolean gates)
... I'd add 1. Use `templateGen`, but you'll need to parse at least one sample to generate a GatingSet. Write the output to file and fill in the missing details. The generated template is just a skeleton. 2. The `polyFunctions` gate may be what you are looking for, as it will generate all boolean com ...
written 2.9 years ago by Greg Finak150
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Answer: A: Load csf files with read.flowSet()
... Hi, Luigi The solution here is not as mysterious as it appears. You see that read.flowSet takes some parameters (the vector of fcs file names) and reads them in. In your case you are reading in the files stored `file.location` but you would like to read in the files stored in `sample.set`. Simply ...
written 3.0 years ago by Greg Finak150
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Answer: A: FlowViz working though is showing as attached
... Did you explicitly `library(flowViz)`? Also, `plot` is not how you plot a flowSet in `flowViz`. You'll want `xyplot`, and you'll want to specify the channels. Have a look at the package vignette here http://www.bioconductor.org/packages/release/bioc/vignettes/flowViz/inst/doc/filters.html It provi ...
written 3.0 years ago by Greg Finak150
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Answer: A: data() doesn't work for fcs files?
... Following up on what Martin has said, read.FCS has already loaded your data into R. You don't need to call data(). As Martin said, that is used to load data sets that are distributed with packages. Your data is already available in the flowFrame object named fcs. What warnings were you getting from ...
written 3.0 years ago by Greg Finak150
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News: New Flow Cytometry Data Analysis Framework
... Hi, everyone We wanted to let list members know that there is a new general framework for performing flow cytometry data analysis in R. The package is called openCyto. The framework has the following features Importing and analyze manually gated data from FlowJo workspace files using the flowWor ...
flowcytometry flowcore opencyto new news written 3.2 years ago by Greg Finak150

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Scholar 2.7 years ago, created an answer that has been accepted. For A: How are autofluorescence values used in the spillover/compensate functions?

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