Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error:
Loading required package: impute
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
1: package ‘samr’ was built under R version 3.3.3
2: package ‘matrixStats’ was built under R version 3.3.3
> samfit<-SAMseq(data, PFI.time,censoring.status=PFI.status, resp.type="Survival")
Estimating sequencing depths...
Error in quantile.default(prop, c(0.25, 0.75)) :
missing values and NaN's not allowed if 'na.rm' is FALSE
In addition: Warning message:
In sum(x) : integer overflow - use sum(as.numeric(.))
Error during wrapup: cannot open the connection
I checked, my data matrix and y variables have no missing values. Anyone has suggestions what's going on?