[NMF-user] NMF v0.20.5 on OS X gives a error for consensusmap(res)

[Gordon Robertson]

To test this further, I did the following, following the user guide vignette PDF. I used RStudio (which I do not use for production NMF runs, but did for this quick test):

data("esGolub")
esGolub <- esGolub[1:200, ]
esGolub$Sample <- NULL
res <- nmf(esGolub, 3) # finished very quickly
res #matches vignette
fit(res) #matches vignette
V.hat <- fitted(res)
dim(V.hat) #matches vignette
summary(res) #matches vignette
summary(res, target = esGolub) #matches vignette
w <- basis(res)
dim(w)

consensusmap(res) #generates a membership heatmap graphic

> coefmap(res)
Error in process_tracks(x, tracks, annRow, annCol) :
  Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.

> basismap(res)
Error in process_tracks(x, tracks, annRow, annCol) :
  Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.

So I seem able to generate a membership heatmap, but not the other two graphics. Until today, I've been able to generate all three.

It's a puzzle.

Gordon
--
Gordon Robertson
Canada's Michael Smith Genome Sciences Centre
BC Cancer Agency
Vancouver BC Canada
www.bcgsc.ca<http://www.bcgsc.ca>
T: 604-707-5900 x675416
Skype: a.gordon.robertson




On 2015-05-22, at 12:23 PM, Gordon Robertson wrote:

Renaud,

On Mac OS X 10.7.5, using R 3.1.3, I'm suddenly getting error messages when I ask for a consensus map, basis map, or coefmap.

This is puzzling, as I've used NMF for months without getting these errors.

I re-installed NMF (from RStudio), then rebooted the Mac, then reran the small demo clustering job below. I get the same errors regardless of whether I run in RStudio (e.g. for the tiny demo), or in a Mac Terminal (where I typically run NMF on 7 of 8 threads on an i7 CPU).

Can you offer any insights?

Thank you -

> n <- 50;
> counts <- c(5, 5, 8);
> V <- syntheticNMF(n, counts, noise=TRUE)
> res <- nmf( V, 3, nrun=8, .options='tvP', .pbackend=4 )
NMF algorithm: 'brunet'
Multiple runs: 8
Mode: parallel (4/8 core(s))
Runs: |==================================================| 100%
System time:
   user  system elapsed
  2.282   0.336   1.285
> consensusmap(res)
Error in process_tracks(x, tracks, annRow, annCol) :
  Invalid special annotation track name ['basis:', 'consensus:', 'silhouette:']. Should partially match one of 'basis:', 'consensus:', 'silhouette:'.
> basismap(res)
Error in process_tracks(x, tracks, annRow, annCol) :
  Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.
> coefmap(res)
Error in process_tracks(x, tracks, annRow, annCol) :
  Invalid special annotation track name ['basis', 'consensus:']. Should partially match one of 'basis', 'consensus:', ':basis', 'basis:'.


> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.7.5 (Lion)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
 [1] doParallel_1.0.8    iterators_1.0.7     foreach_1.4.2       NMF_0.20.5          Biobase_2.26.0      BiocGenerics_0.12.1
 [7] cluster_2.0.1       rngtools_1.2.4      pkgmaker_0.22       registry_0.2

loaded via a namespace (and not attached):
 [1] codetools_0.2-11   colorspace_1.2-6   compiler_3.1.3     digest_0.6.8       ggplot2_1.0.1      grid_3.1.3         gridBase_0.4-7
 [8] gtable_0.1.2       magrittr_1.5       MASS_7.3-40        munsell_0.4.2      plyr_1.8.2         proto_0.3-10       RColorBrewer_1.1-2
[15] Rcpp_0.11.5        reshape2_1.4.1     scales_0.2.4       stringi_0.4-1      stringr_1.0.0      tools_3.1.3        xtable_1.7-4
>

Gordon
--
Gordon Robertson
Canada's Michael Smith Genome Sciences Centre
BC Cancer Agency
Vancouver BC Canada
www.bcgsc.ca<http://www.bcgsc.ca/>
T: 604-707-5900 x675416
Skype: a.gordon.robertson





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