Error in zlm function model matrix
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Entering edit mode
jka8119 ▴ 10
@jka8119-15080
Last seen 21 months ago

Hi,

I getting an error below with MAST:

scaRaw <- FromMatrix(as.matrix(fibronorm), fibroidentities, subset(genes, genes$primerid %in% row.names(fibronorm)))
cdr2 <-colSums(assay(scaRaw)>0)
colData(scaRaw)$cngeneson <- scale(cdr2)

cond<-factor(colData(scaRaw)$proinflammatoryvector)
cond<-relevel(cond,"cd55low")
colData(scaRaw)$condition<-cond
zlmCond <- zlm(~condition+cngeneson, scaRaw)

Error in object@modelMatrix[pos, , drop = FALSE] :
  (subscript) logical subscript too long

 

Not sure what the reason is. I never encountered this error before when using the zlm function.

>sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

Matrix products: default
BLAS/LAPACK: /local/system/opt/R/3.4.2/lib/libopenblas_nehalemp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] scran_1.6.2                BiocParallel_1.12.0
 [3] scater_1.6.0               ggplot2_2.2.1
 [5] MAST_1.6.0                 SingleCellExperiment_1.0.0
 [7] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
 [9] matrixStats_0.53.1         Biobase_2.38.0
[11] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0
[13] IRanges_2.12.0             S4Vectors_0.16.0
[15] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] dynamicTreeCut_1.63-1   viridis_0.4.0           httr_1.3.1
 [4] edgeR_3.20.1            splines_3.4.2           bit64_0.9-7
 [7] viridisLite_0.2.0       shiny_1.0.5             assertthat_0.2.0
[10] statmod_1.4.30          blob_1.1.0              GenomeInfoDbData_0.99.1
[13] vipor_0.4.5             progress_1.1.2          RSQLite_2.0
[16] lattice_0.20-35         glue_1.2.0              limma_3.34.1
[19] digest_0.6.12           XVector_0.18.0          colorspace_1.3-2
[22] htmltools_0.3.6         httpuv_1.3.5            Matrix_1.2-11
[25] plyr_1.8.4              XML_3.98-1.9            pkgconfig_2.0.1
[28] biomaRt_2.34.2          zlibbioc_1.24.0         xtable_1.8-2
[31] scales_0.5.0            tibble_1.3.4            DT_0.2
[34] lazyeval_0.2.1          magrittr_1.5            mime_0.5
[37] memoise_1.1.0           FNN_1.1                 beeswarm_0.2.3
[40] shinydashboard_0.6.1    tools_3.4.2             data.table_1.10.4-3
[43] prettyunits_1.0.2       stringr_1.2.0           munsell_0.4.3
[46] locfit_1.5-9.1          AnnotationDbi_1.40.0    bindrcpp_0.2
[49] compiler_3.4.2          rlang_0.1.4             rhdf5_2.22.0
[52] grid_3.4.2              RCurl_1.95-4.8          tximport_1.6.0
[55] htmlwidgets_0.9         rjson_0.2.15            igraph_1.2.1
[58] bitops_1.0-6            gtable_0.2.0            abind_1.4-5
[61] DBI_0.7                 reshape2_1.4.2          R6_2.2.2
[64] zoo_1.8-0               gridExtra_2.3           dplyr_0.7.4
[67] bit_1.1-12              bindr_0.1               stringi_1.1.5
[70] ggbeeswarm_0.6.0        Rcpp_0.12.16

MAST • 538 views
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It looks like you have a mismash of Bioconductor 3.7 and 3.6.  What does `BiocInstaller::biocValid()` report?  Did you install MAST off of github, or via Bioconductor?

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Thanks. I installed the source package using 'install.packages'. BiocInstaller::biocValid() reports it to be too new.

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Yup.  Downgrade MAST to version 1.4.1 (here: http://bioconductor.org/packages/3.6/bioc/html/MAST.html) or upgrade to R 3.5 and Bioconductor 3.7.

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Still getting the same issue after reinstalling MAST (v 1.4.1). Perhaps i am having an issue with the version of limma i have?

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Restart R, verify that you are running bioconductor 3.6 with BiocInstaller::biocValid() and make sure you aren't reloading from disk any "stale" objects that were created when you had mismatched package versions.  Checking that you can run the equivalent code in the MAITAnalysis vignette should serve a positive control.  I still suspect version mismatching of some sort is at fault here.

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I ended up upgrading to Bioconductor 3.7 and R 3.5, MAST 1.6.0. That eventually solved the problem. Thanks for the help.

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