[R] SAMseq errors

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Wed Nov 29 18:58:18 CET 2017

A) This list is a general interest list on the R language... you have posed your question as if you were looking for domain experts such as you might be more likely to find on the Bioconductor mailing list. 

B) Example is not reproducible. [1][2][3]

C) Just because your data don't have missing values does not mean that your early analysis steps don't create them, e.g. by taking the logarithm of negative numbers. Look at intermediate values in your analysis, and read the documentation for steps you are treating as "magic black boxes".

[1] http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

[2] http://adv-r.had.co.nz/Reproducibility.html

[3] https://cran.r-project.org/web/packages/reprex/index.html (read the vignette)
Sent from my phone. Please excuse my brevity.

On November 29, 2017 9:39:24 AM PST, array chip via R-help <r-help at r-project.org> wrote:
>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,
>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
>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!
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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