Error message running DE-test in Monocle
1
1
Entering edit mode
Jon Bråte ▴ 180
@jon-brate-6263
Last seen 3 months ago
Norway

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

 

monocle cummerbund DE rnaseq • 1.0k views
ADD COMMENT
0
Entering edit mode
ksekine • 0
@ksekine-8399
Last seen 6.2 years ago
Japan

Hi Jon,

I've got same error.

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

 

Thanks!

ADD COMMENT
0
Entering edit mode

No sorry, have not solved it.. :(
 

ADD REPLY

Login before adding your answer.

Traffic: 208 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6