Question: Error message running DE-test in Monocle
1
gravatar for Jon Bråte
4.7 years ago by
Jon Bråte160
Norway
Jon Bråte160 wrote:

I am using the Monocle package to run DE-tests. I get several error messages running differentialGeneTest, but the testing doesn't stop and produces a sensible outcome. But I wonder what the messages mean? It think it may have something to do with genes having zero expression in some samples. I have 5 samples and chosen genes which are expressed in at least 3.


Some of the messages:

<simpleError in if (any(cenL)) {    mumL <- Lowmat[, spp.] - muvec    temp21L <- mumL[cenL]/sdvec[cenL]    PhiL <- pnorm(temp21L)    phiL <- dnorm(temp21L)    fred21 <- phiL/PhiL    dl.dmu[cenL] <- -fred21/sdvec[cenL]    dl.dsd[cenL] <- fred21 * (-mumL[cenL]/sdvec[cenL]^2)}: missing value where TRUE/FALSE needed>

<simpleError in lm.wfit(x = cbind(x[!use.i11, ]), y = y[!use.i11, ii], w = w[!use.i11,     ii]): incompatible dimensions>

 

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] C

attached base packages:
 [1] splines   grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[11] base     

other attached packages:
 [1] monocle_1.0.0        plyr_1.8.1           igraph_0.7.1         Biobase_2.26.0      
 [5] HSMMSingleCell_1.0.0 VGAM_0.9-7           cummeRbund_2.8.2     Gviz_1.10.10        
 [9] rtracklayer_1.26.2   GenomicRanges_1.18.4 GenomeInfoDb_1.2.4   IRanges_2.0.1       
[13] S4Vectors_0.4.0      fastcluster_1.1.16   reshape2_1.4.1       ggplot2_1.0.0       
[17] RSQLite_1.0.0        DBI_0.3.1            BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1     BBmisc_1.9               BSgenome_1.34.1          BatchJobs_1.5           
 [5] BiocParallel_1.0.3       Biostrings_2.34.1        Formula_1.2-0            GenomicAlignments_1.2.2
 [9] GenomicFeatures_1.18.3   Hmisc_3.15-0             MASS_7.3-39              Matrix_1.1-5            
[13] RColorBrewer_1.1-2       RCurl_1.95-4.5           Rcpp_0.11.5              Rsamtools_1.18.3        
[17] VariantAnnotation_1.12.9 XML_3.98-1.1             XVector_0.6.0            acepack_1.3-3.3         
[21] base64enc_0.1-2          biomaRt_2.22.0           biovizBase_1.14.1        bitops_1.0-6            
[25] brew_1.0-6               checkmate_1.5.1          cluster_2.0.1            codetools_0.2-10        
[29] colorspace_1.2-6         combinat_0.0-8           dichromat_2.0-0          digest_0.6.8            
[33] fail_1.2                 fastICA_1.2-0            foreach_1.4.2            foreign_0.8-63          
[37] gtable_0.1.2             irlba_1.0.3              iterators_1.0.7          labeling_0.3            
[41] lattice_0.20-30          latticeExtra_0.6-26      limma_3.22.7             matrixStats_0.14.0      
[45] munsell_0.4.2            nnet_7.3-9               proto_0.3-10             rpart_4.1-9             
[49] scales_0.2.4             sendmailR_1.2-1          stringr_0.6.2            survival_2.38-1         
[53] tools_3.1.3              zlibbioc_1.12.0

 

rnaseq cummerbund monocle de • 872 views
ADD COMMENTlink modified 4.4 years ago by ksekine0 • written 4.7 years ago by Jon Bråte160
Answer: Error message running DE-test in Monocle
0
gravatar for ksekine
4.4 years ago by
ksekine0
Japan
ksekine0 wrote:

Hi Jon,

I've got same error.

If you have solved the problem, please let me know.

 

Thanks!

ADD COMMENTlink written 4.4 years ago by ksekine0

No sorry, have not solved it.. :(
 

ADD REPLYlink written 4.4 years ago by Jon Bråte160
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