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gabor.halasz
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@gaborhalasz-12176
Last seen 7.9 years ago
Dear all,
I'm getting the following error when running the SampleAnalysis vignette of the CellMix package:
library(CellMix)
biocLite("GEOquery")
acr <- ExpressionMix("GSE20300", verbose = 2)
res <- gedBlood(acr, verbose = 2);
###...skipping most of the output...
###Normalizing signatures and target together (method: quantiles) ... OK
Error in (function (od, vd) :
object and replacement value dimnames differ
biocVersion() is 3.4, and my sessionInfo() is:
R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El Capitan) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats4 compiler parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.40.0 hgu133b.db_3.2.3 hgu133a.db_3.2.3 org.Hs.eg.db_3.4.0 [5] CellMix_1.6.2 GSEABase_1.36.0 graph_1.52.0 annotate_1.52.1 [9] XML_3.98-1.5 AnnotationDbi_1.36.1 IRanges_2.8.1 S4Vectors_0.12.1 [13] stringr_1.1.0 csSAM_1.2.4 NMF_0.20.6 Biobase_2.34.0 [17] BiocGenerics_0.20.0 cluster_2.0.4 rngtools_1.2.4 pkgmaker_0.22 [21] registry_0.3 BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] genefilter_1.56.0 gtools_3.5.0 beeswarm_0.2.3 lpSolve_5.6.13 [5] reshape2_1.4.2 splines_3.3.1 lattice_0.20-33 limSolve_1.5.5.1 [9] colorspace_1.3-2 survival_2.40-1 DBI_0.5-1 RColorBrewer_1.1-2 [13] matrixStats_0.51.0 foreach_1.4.3 plyr_1.8.4 munsell_0.4.3 [17] gtable_0.2.0 codetools_0.2-15 memoise_1.0.0 doParallel_1.0.10 [21] preprocessCore_1.36.0 Rcpp_0.12.9 xtable_1.8-2 corpcor_1.6.8 [25] scales_0.4.1 ggplot2_2.2.1 digest_0.6.11 stringi_1.1.2 [29] grid_3.3.1 bibtex_0.4.0 quadprog_1.5-5 tools_3.3.1 [33] bitops_1.0-6 magrittr_1.5 lazyeval_0.2.0 RCurl_1.95-4.8 [37] tibble_1.2 RSQLite_1.1-2 MASS_7.3-45 Matrix_1.2-6 [41] gridBase_0.4-7 httr_1.2.1 assertthat_0.1 iterators_1.0.8 [45] R6_2.2.0
Any help would be greatly appreciated. Thanks,
Gabor
Note, the function does work if you explicitly pass it the expression matrix directly rather than the
acrExpressionMix class object:Thank you so much!! Passing in the expression matrix directly works for me as well. (And otherwise yes, that is the line that breaks, and it may work with previous Biobase versions).
I've found exactly the same thing.
The error seems to be coming from a validation check in the Biobase package: https://github.com/Bioconductor-mirror/Biobase/blob/master/R/methods-eSet.R#L461
I ran debug on
gedBlood()and thengedProportions()and found that it happens on this line of code: https://github.com/rforge/cellmix/blob/master/pkg/CellMix/R/ged.R#L769 . It seems a strange error as the previous line tries to set thedimnamesequal to each other.Perhaps a compatibility issue with a new version of Biobase? The vignette says it uses Biobase 2.20.0. I haven't been able to confirm this by installing that old version of Biobase - anyone know an easy way to do that?
I have emailed the package maintainer last week but haven't heard back yet.
Graeme