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: imputeLoading 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 FALSEIn 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
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