Question

SAMseq error message

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array chip ▴ 420

@array-chip-4136

Last seen 10 months ago

United States

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

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

Thank you!

John

SAMSeq • 1.8k views

ADD COMMENT • link 7.0 years ago array chip ▴ 420

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Here is the info from

> biocValid()

[1] TRUE

> 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

ADD REPLY • link 7.0 years ago array chip ▴ 420

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Hello array chip!

It appears that your post has been cross-posted to another site: Asked elsewhere https://stat.ethz.ch/pipermail/r-help/2017-November/450287.html

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLY • link 7.0 years ago Martin Morgan 25k

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sorry that I realized that samr package is in the R community, instead of bioconductor, so I posted it there again. Sorry if this annoys anyone. But would really appreciate if anyone responds if knowing what's going on with the error.

ADD REPLY • link 7.0 years ago array chip ▴ 420

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someone suggest this question is better answered on bioconductor, instead of in R community. so here is more info from what I have been trying:

I did not do any pre-processing (normalization/transformation) and used raw counts in the SAMseq(). I tried to reduce the size of input data. I found out that SAMseq runs fine with the first 1457 genes, but ran into the problem when 1458 genes are used. But I found no problem with raw counts from the 1458th gene. And when I run SAMseq() on the next 1268 genes separately, it works fine, too. So it's not that the 1458th gene has anything wrong! SAMseq() ran into problem again when I ran the next 1269 genes separately.

At this point, I think it is something internal with SAMseq that prevent its working on large matrix input data. Just noticed that its last release is in 2011.

ADD REPLY • link 7.0 years ago array chip ▴ 420

score 0 · Answer 1 · 2017-11-29

As Martin already pointed out, samr is a CRAN package, not Bioconductor, so by definition it is not better answered here, since neither the authors nor maintainers are expected to watch posts at this site. Just because samr is supposed to have similar functionality as certain Bioconductor packages doesn't mean anybody here can help.

As you have noted, samr isn't necessarily regularly maintained. Whereas packages like DESeq2 and edgeR are not only regularly maintained, the people who maintain those packages are some of the most active posters on this here site. You might have a compelling reason to use samr, in which case you can try on stackoverflow, biostars, or r-help. Otherwise, you might consider using something that is both maintained and supported.

score 0 · Answer 2 · 2017-11-29

Thank you James. Unfortunately, I am trying to use survival analysis with RNA-seq data. Michael Love previously (in my another thread earlier) has suggested to use SAMseq for that purpose, because DESeq2 and edgeR do not work for survival models (wish this functionality can be added in the future). I may have to do vst transformation and then run survival analysis separately... Thanks anyway.