[aroma.affymetrix] Running multiple pairs through Paired PSCBS

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[aroma.affymetrix] Running multiple pairs through Paired PSCBS

Gaius Augustus
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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[aroma.affymetrix] Re: Running multiple pairs through Paired PSCBS

Amy Sherborne
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 <a href="http://www.aroma-project.org/vignettes/PairedPSCBS-lowlevel/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2Fvignettes%2FPairedPSCBS-lowlevel%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEwNGmsbGfKMBv5W9sgpDEOMCVo_g&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2Fvignettes%2FPairedPSCBS-lowlevel%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEwNGmsbGfKMBv5W9sgpDEOMCVo_g&#39;;return true;">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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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.
 
 
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