[BioC] Help with flowCore

[Mike]

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
> --------------------------------------------------------------------------
> LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO.
> AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 07636600962
> info:www.5xmille at hsr.it - www.5xmille.org
>
> Disclaimer added by CodeTwo Exchange Rules 2007
> http://www.codetwo.com
>