[BioC] Help with flowCore

Mike wjiang2 at fhcrc.org
Thu Apr 4 18:50:11 CEST 2013



Andrea,

We should compensate the data outside of read.flowSet call. Here is what
you can do:

#read the FCS files into a flowSet
fs <- read.flowSet(...)

#loop through flowset and do the compensation for each flowFrame
#and return the compensated flowFrame,fsApply call will construct a new
flowSet for you

fs_comp <- fsApply(fs,function(frame){
     #extract compensation matrix from keywords
     comp <- keyword(frame)$`SPILL`
     new_frame <- compensate(frame,comp)
     new_frame
})

Let me know if you have more questions.

Mike
On 04/03/2013 03:43 AM, Valle Andrea wrote:
> Dear Dr. Jiang,
>
> I'm a PhD student in Milan and I'm trying flowCore package. First of all let me tell you that I think it has been a great step forward in flow cytometry!
> I'm writing you cause I have an issue about compensation and, although I tried a lots of possible solutions, I didn't succeed. I have to say that I'm not an expert in R langauge since this is my first approach with this subject.
> When I load an FCS file it's is not compensated, although it include $SPILL matrix. Of course I can use "compensate" to apply the $SPILL matrix to that file. However I can't do it upon flowset creation. Once I created a flowset, the $SPILL keyword is no more included in each file.
> How can I create a flowset in which each file is automatically compensated with its own compensation?
>
> I attached a representative file
>
> Many many thanks!
>
> Andrea Valle
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