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 locale: [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! John ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
