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: https://github.com/Sherbornator/Affy/blob/master/PairedPSCBS.R 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 > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to firstname.lastname@example.org To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.