Hi Gaius,

I have just written an R script to do exactly the thing you you are asking 
about, I hope it helps.

Instead of calling the Tumor and Normal separately within the loop, I put 
them into a data frame and then just recalled the entire row - that way I 
had to change very little of the code from the PairedPSCBS vignette.

Using your example:
T <- c("Sample1_T.CEL", "Sample2_T.CEL", "Sample3_T.CEL") 
N <- c("Sample1_N.CEL", "Sample2_N.CEL", "Sample3_N.CEL") 
pair = data.frame(T, N, stringsAsFactors=F)

Then within my for loop I called csR <- csR[indexOf(csR, pair[i,])].

Full code is up on my github:

On Thursday, 9 June 2016 19:31:29 UTC+1, Gaius Augustus wrote:
> Hello,
> I have a few hundred paired samples that I'd like to run through Paired 
> PSCBS.  The example at 
> http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/ is very 
> clear on how to set up this protocol for one pair of samples.  In order to 
> do a test run, I used a for loop to run Paired PSCBS on each pair one at a 
> time.
> Is there another way to do this?
> For example, I have two vectors with file names
> TumorSamples <- c("Sample1_T.CEL", "Sample2_T.CEL", "Sample3_T.CEL")
> NormalSamples <- c("Sample1_N.CEL", "Sample2_N.CEL", "Sample3_N.CEL")
> instead of pair <- c(T="GSM318736", N="GSM318737")
> within a for loop, I ran TumorNormalpair <- c(T=dsT[i], N=dsN[i])
> Thanks,
> Gaius

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