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