<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Renaud,</div><div><br></div>Thank you for this lightning-fast response! I think I did update stringr last week. I'll update and will retry it. <div><br></div><div>Gordon<br><div apple-content-edited="true">
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<br><div><div>On 2015-05-22, at 12:59 PM, Renaud wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">This comes from a change in stringr, which you probably updated.<div>This is fixed in the master and devel branch on GitHub. You can install from there to get it right <span></span>now.<br><div>I will push the fix to CRAN on Monday.</div><div><br></div><div>Bests,</div><div>Renaud<br><br>On Friday, May 22, 2015, Gordon Robertson <<a href="mailto:grobertson@bcgsc.ca">grobertson@bcgsc.ca</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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):<div><br></div><div><div>data("esGolub")</div><div>esGolub <- esGolub[1:200, ]</div><div>esGolub$Sample <- NULL</div><div>res <- nmf(esGolub, 3) # finished very quickly</div><div>res #matches vignette</div><div>fit(res) #matches vignette</div><div>V.hat <- fitted(res)</div><div>dim(V.hat) #matches vignette</div><div>summary(res) #matches vignette</div><div>summary(res, target = esGolub) #matches vignette</div><div>w <- basis(res)</div><div>dim(w)</div><div><br></div><div>consensusmap(res) #generates a membership heatmap graphic</div><div><div><br></div><div>> coefmap(res)</div><div><font color="#db5127">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font color="#db5127"> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.</font></div><div><br></div><div>> basismap(res)</div><div><font color="#db5127">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font color="#db5127"> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.</font></div></div><div><br></div><div>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. </div><div><br></div><div>It's a puzzle. </div><div><br></div><div>Gordon</div><div>
<div style="word-wrap:break-word"><div style="word-wrap:break-word"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div style="word-wrap:break-word"><div><div>--</div><div>Gordon Robertson</div><div>Canada's Michael Smith Genome Sciences Centre</div><div>BC Cancer Agency </div><div>Vancouver BC Canada</div><div><a href="http://www.bcgsc.ca/" target="_blank">www.bcgsc.ca</a></div></div><div><div>T: 604-707-5900 x675416</div><div>Skype: a.gordon.robertson</div></div><div><br></div></div></span></div></div><br><br>
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<br><div><div>On 2015-05-22, at 12:23 PM, Gordon Robertson wrote:</div><br><blockquote type="cite"><div style="word-wrap:break-word"><div>Renaud,</div><div><br></div><div>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. </div><div><br></div><div>This is puzzling, as I've used NMF for months without getting these errors. </div><div><br></div><div>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). </div><div><br></div><div>Can you offer any insights? </div><div><br></div><div>Thank you -</div><div><br></div><div><div>> n <- 50;</div><div>> counts <- c(5, 5, 8);</div><div>> V <- syntheticNMF(n, counts, noise=TRUE)</div><div>> res <- nmf( V, 3, nrun=8, .options='tvP', .pbackend=4 )</div><div>NMF algorithm: 'brunet'</div><div>Multiple runs: 8</div><div>Mode: parallel (4/8 core(s))</div><div>Runs: |==================================================| 100%</div><div>System time:</div><div> user system elapsed </div><div> 2.282 0.336 1.285 </div><div>> consensusmap(res)</div><div><font color="#db5127">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font color="#db5127"> Invalid special annotation track name ['basis:', 'consensus:', 'silhouette:']. Should partially match one of 'basis:', 'consensus:', 'silhouette:'.</font></div></div><div><div>> basismap(res)</div><div><font color="#db5127">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font color="#db5127"> Invalid special annotation track name ['basis']. Should partially match one of 'basis', ':basis', 'basis:'.</font></div></div><div><div>> coefmap(res)</div><div><font color="#db5127">Error in process_tracks(x, tracks, annRow, annCol) : </font></div><div><font color="#db5127"> Invalid special annotation track name ['basis', 'consensus:']. Should partially match one of 'basis', 'consensus:', ':basis', 'basis:'.</font></div></div><div><br></div><div><br></div><div><div>> sessionInfo()</div><div><font color="#db5127">R version 3.1.3 (2015-03-09)</font></div><div>Platform: x86_64-apple-darwin10.8.0 (64-bit)</div><div>Running under: OS X 10.7.5 (Lion)</div><div><br></div><div>locale:</div><div>[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8</div><div><br></div><div>attached base packages:</div><div>[1] parallel stats graphics grDevices utils datasets methods base </div><div><br></div><div>other attached packages:</div><div> [1] doParallel_1.0.8 iterators_1.0.7 foreach_1.4.2 <font color="#db5127">NMF_0.20.5</font> Biobase_2.26.0 BiocGenerics_0.12.1</div><div> [7] cluster_2.0.1 rngtools_1.2.4 pkgmaker_0.22 registry_0.2 </div><div><br></div><div>loaded via a namespace (and not attached):</div><div> [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 </div><div> [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</div><div>[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 </div><div>> </div></div><div><br></div><div>Gordon</div><div>
<div style="word-wrap:break-word"><div style="word-wrap:break-word"><div style="word-wrap:break-word"><div><div>--</div><div>Gordon Robertson</div><div>Canada's Michael Smith Genome Sciences Centre</div><div>BC Cancer Agency </div><div>Vancouver BC Canada</div><div><a href="http://www.bcgsc.ca/" target="_blank">www.bcgsc.ca</a></div></div><div><div>T: 604-707-5900 x675416</div><div>Skype: a.gordon.robertson</div></div><div><br></div></div></div></div><br><br>
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