Thanks for the advice Mike. I have tried changing the fsc/ssc calls 
around as you suggested, and get the same error. On the bright side, I 
was able to use spillover() successfully with the sample data in 
flowCore/extdata/compdata/data. I reckon my flowSet needs some cleaning 
up yet. -k

On 11/06/2012 04:06 PM, Mike wrote:
> Hi,Kevin,
>
> Your spillover call should go like this:
> spill.mat<- spillover(comp.data,..., fsc="FSC-A", ssc="SSC-A")
>
> Regarding to importing flowJo xml to R,you can try "flowWorkspace" package. Hope this helps.
>
>
> Mike Jiang,PhD
>
> System Analyst
>
> PS Statistics, Vaccine and Infectious Disease Division
>
> Fred Hutchinson Cancer Research Center
>
> (206)667-1905  <tel:%28206%29667-1905>
>
>
> On 11/06/2012 03:06 PM, Kevin Schiesser [guest] wrote:
>> Hello there,
>> I am using Bioconductor to look at flow cytometry data. To begin, I would like to generate and apply a compensation matrix to the experimental samples. Below is the work flow, as well as more general information on the flowSet and the R version that I use. Any recommendations would be splendid. I am thinking I might have to figure on how to import FlowJo 10 xml files into bionconductor, a step that I prefer to avoid.
>>
>> Much thanks,
>> Kevin
>>
>> PS I have tried many permutations of the spillover() method including patt=..., useNormFilt=TRUE/FALSE, changing the unstained = index around, etc... And also, I cannot seem to get system.file("compC", package="flowCore") to return a non-empty value, maybe that would make compensation easier. Just a thought. -k
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> ##import the flowSet
>>
>> library(flowCore)
>>
>> compData<- read.flowSet(path = ".../compC/", transformation = FALSE)
>>
>> ##trim the time column off (I know there are faster ways, but to be very explicit...)
>>
>> comp.data<- compData[c(1,2,3,4,5,6,7,8,9,10,11,12),c("FSC-A", "SSC-A", "FITC-A", "PerCP-A", "Pacific Blue-A", "AARD-A", "QDot605-A", "APC-A", "Alexa700-A", "APC-Cy7-A", "PE-A", "ECD-A", "PE-Cy7-A")]
>>
>> ##generate compensation matrix
>>
>> spill.mat<- spillover(comp.data,unstained = sampleNames(compData)[12], fsc=compData[,1], ssc=compData[,2])
>>
>>> traceback()
>> 3: .local(x, ...) : subscript out of bounds
>> 2: spillover(comp.data, unstained<- sampleNames(compData)[12], fsc = compData[,1], ssc = compData[, 2])
>> 1: spillover(comp.data, unstained<- sampleNames(compData)[12], fsc = compData[,1], ssc = compData[, 2])
>>
>>> compData[[12]]
>> flowFrame object 'Compensation Controls_Unstained Control.fcs'
>> with 10000 cells and 14 observables:
>>                 name desc  range minRange maxRange
>> $P1           FSC-A   NA 262144     0.00   262143
>> $P2           SSC-A   NA 262144     0.00   262143
>> $P3          FITC-A   NA 262144  -106.22   262143
>> $P4         PerCP-A   NA 262144  -111.00   262143
>> $P5  Pacific Blue-A   NA 262144  -111.00   262143
>> $P6          AARD-A   NA 262144  -111.00   262143
>> $P7       QDot605-A   NA 262144  -111.00   262143
>> $P8           APC-A   NA 262144   -29.05   262143
>> $P9      Alexa700-A   NA 262144   -82.17   262143
>> $P10      APC-Cy7-A   NA 262144  -111.00   262143
>> $P11           PE-A   NA 262144   -87.69   262143
>> $P12          ECD-A   NA 262144   -63.27   262143
>> $P13       PE-Cy7-A   NA 262144   -25.53   262143
>> $P14           Time   NA 262144     0.00   262143
>> 182 keywords are stored in the 'description' slot
>>
>>   -- output of sessionInfo():
>>
>>> sessionInfo()
>> R version 2.15.1 (2012-06-22)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=C                 LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] flowCore_1.24.0    rrcov_1.3-02       pcaPP_1.9-48       mvtnorm_0.9-9993
>> [5] robustbase_0.9-4   Biobase_2.18.0     BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] feature_1.2.8 graph_1.36.0  ks_1.8.10     MASS_7.3-22   stats4_2.15.1
>> [6] tools_2.15.1
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>


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