Question: How can I run a paired RankProd analysis in R?
gravatar for joker33
10 months ago by
joker330 wrote:

Hi! I would like to run a paired RankProd analysis in R. My dataset consists of paired cancer samples and healthy controls. For example, the Colorectal Cancer data set consists of 40 cancer samples and 40 paired healthy controls. I defined the class vectors and origin vectors accordingly:

class vector

n1 <- 40 n2 <- 40 cl <- rep(c(0,1), c(n1,n2))

origin vector

origin <- rep(1, n1+n2)

rankprod code

RP.out <- RankProducts(cancer_data, cl, origin, logged=TRUE, plot=FALSE, gene.names = genenames, rand=123)

I have two questions: 1. This calculation will always run as "Rank Product analysis for unpaired case". Is there a specific argument where I can specify the pairing of my cancer samples and healthy controls?

  1. If I run a dataset with more than 60 samples (30 cancer + 30 healthy controls), I receive an error message that reads: "Error: vector memory exhausted (limit reached?)" (NB: I use a MAC). I've followed some advice from other forums to change .Renviron file to "R_MAX_VSIZE=100GB". But with those large matrices, the error does not go away. Is there any solution?

Thank you very much for your help in advance, Cheers

rna-seq R • 299 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by joker330
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