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
No sorry, have not solved it.. :(