[BioC] spillover method in flowCore package

Frederico Arnoldi fredgca at hotmail.com
Sat Mar 27 22:25:02 CET 2010

Dear Nishant,

Thanks for helping me! And sorry for sending the email in HTML for the list. 

> 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 ? 

In fact, I just have 5 stained channels. I my previous email "PE Cy7-A"  looked like two dyes instead of one. 

> colnames(fs)
[1] "FSC-H"    "SSC-A"    "FITC-A"   "PE-A"     "PerCP-A"  "PE Cy7-A" "APC-A"   
[8] "Time" 

When I use the following command, the Time column is eliminated, as we can see in the output. 

> fs[,1:7]
A flowSet with 6 experiments.

  column names:

However, when I use it in the spillover method, I still having the same error. 

> comp.mat <- spillover(fs[,1:7], unstained=1, fsc = "FSC-H", ssc= "SSC-A")
Error in .local(x, ...) : subscript out of bounds

Thanks again,

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