[R] SAMseq errors

array chip arrayprofile at yahoo.com
Wed Nov 29 18:39:24 CET 2017

Sorry forgot to use plain text format, hope this time it works:

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:

> library(samr)
Loading required package: impute
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Warning messages:
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

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] samr_2.0             matrixStats_0.52.2   impute_1.48.0        BiocInstaller_1.24.0 rcom_3.1-3           rscproxy_2.1-1      

loaded via a namespace (and not attached):
[1] tools_3.3.2

I checked, my data matrix and y variables have no missing values. Anyone has suggestions what's going on?

Thank you!


More information about the R-help mailing list