Hi Frederico,

Your flowSet  appears to have 1 unstained sample and 5 single stained
controls for 
APC, PercPCy5.5, FITC, PeCy7 and PE . The column names of fs have
FITC-A, PE-A, PerCP-A, PE, Cy7-A and APC-A ( 6 channels).

Can you try to call spillover after removing  the columns corresponding
to Time and the missing channel for which you do not have single stained
samples for from the flowSet ?

Nishant


On 03/26/2010 08:01 AM, Frederico Arnoldi wrote:
> Dear list,
>
> I am having problems with the "spillover" method of the flowCore package. I am trying to compensate a flowset but everytime I tried to get the spillover matrix from my control data, I received the following error message:
>
> "Error in .local(x, ...) : subscript out of bounds"
>
> In my flowset I have 6 flowframes (in the following order: unstained cells, APC, PercPCy5.5, FITC, PeCy7, PE) that I have loaded as following: 
>
>   
>> library("flowCore")
>> library("flowViz")
>> fs = read.flowSet(path = "path")
>> fs
>>     
> A flowSet with 6 experiments.
>
>   column names:
>   FSC-H SSC-A FITC-A PE-A PerCP-A PE Cy7-A APC-A Time
>
>
> I tried to get the spillover matrix with
>
>   
>> comp.mat <- spillover(fs, unstained=1, fsc = "FSC-H", ssc= "SSC-A")
>>     
> Error in .local(x, ...) : subscript out of bounds
>
> I can not identify where is my mistake. I tried a fast look in the source code of "spillover method" (starting at line 525 of the flowSet-accessors.R in the flowCore_1.8.3.tar.gz), but I also not able to identify the source of my error or a possible bug.
>
> Please, could anyone help me with it?
>
> Thanks in advance,
> Fred 		 	   		  
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