Entering edit mode
hi all
I'm using MAST to run DEG analysis for treated vs. untreated samples.
I use the following code:
cond <- factor(df$Group) cond <- relevel(cond, "CTR")
colData(sca)$condition <- cond
zlmCond <- zlm(~ condition, sca)
followign the example here: https://bioconductor.org/packages/release/bioc/vignettes/MAST/inst/doc/MAITAnalysis.html#4differentialexpressionusingahurdlemodel
however, when I have to run lrTest with:
summaryCond <- summary(zlmCond, doLRT='conditionTREAT')
I get the following error:
invalid class “Hypothesis” object: superclass "characterORconnection" not defined in the environment of the object's class
my colData(sca) look like this:
DataFrame with 3872 rows and 2 columns
wellKey condition
<character> <factor>
CTR_CC30_CC30_TAGAGTCCACCCAATA-1 CTR_CC30_CC30_TAGAGT.. CTR
CTR_CC30_CC30_CCTAACCAGCTAGCCC-1 CTR_CC30_CC30_CCTAAC.. CTR
CTR_CC30_CC30_CTACCCAGTGACACGA-1 CTR_CC30_CC30_CTACCC.. CTR
CTR_CC30_CC30_TGACCCTCACTAGTAC-1 CTR_CC30_CC30_TGACCC.. CTR
CTR_CC30_CC30_GGGACCTGTACTGAGG-1 CTR_CC30_CC30_GGGACC.. CTR
... ... ...
TREAT_TG1_AGCGTCGTCGGCTGAC-1 TREAT_TG1_AGCGTCGTC.. TREAT
TREAT_TG1_TTGACCCCACTTGACA-1 TREAT_TG1_TTGACCCCA.. TREAT
TREAT_TG1_TTGCATTGTTCCAAAC-1 TREAT_TG1_TTGCATTGT.. TREAT
TREAT_TG1_GTCGTAAGTCACTCTC-1 TREAT_TG1_GTCGTAAGT.. TREAT
TREAT_TG1_ACGGGTCGTATCGTGT-1 TREAT_TG1_ACGGGTCGT.. TREAT
and my zlmCond looks as follows:
print(summary(zlmCond), n=5)
Combining coefficients and standard errors
Calculating log-fold changes
Fitted zlm with top 5 genes per contrast:
( log fold change Z-score )
primerid conditionTREAT
Elf4_(+) 5.8*
Ep300_(+) 5.7*
Ikzf1_(+) 6.1*
Stat1_(+) 6.1*
Stat2_(+) 5.5*
I tried re-installing MAST and restarting the R session but it didn't help...
traceback()
gives:
15: h(simpleError(msg, call))
14: .handleSimpleError(function (cond)
.Internal(C_tryCatchHelper(addr, 1L, cond)), "invalid class “CoefficientHypothesis” object: superclass \"characterORconnection\" not defined in the environment of the object's class",
base::quote(validObject(.Object)))
13: stop(msg, ": ", errors, domain = NA)
12: validObject(.Object)
11: initialize(value, ...)
10: initialize(value, ...)
9: new(whoami, .Data = hypothesis)
8: CoefficientHypothesis(x)
7: lrTest(object, CoefficientHypothesis(x))
6: FUN(X[[i]], ...)
5: lapply(doLRT, function(x) lrTest(object, CoefficientHypothesis(x))[,
, "Pr(>Chisq)"])
4: lapply(doLRT, function(x) lrTest(object, CoefficientHypothesis(x))[,
, "Pr(>Chisq)"])
3: .local(object, ...)
2: summary(zlmCond, doLRT = "conditionTREAT")
1: summary(zlmCond, doLRT = "conditionTREAT")
and sessionInfo() is:
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] MAST_1.15.0 SingleCellExperiment_1.11.6 SummarizedExperiment_1.19.6
[4] DelayedArray_0.15.7 matrixStats_0.56.0 Matrix_1.2-18
[7] Biobase_2.49.0 GenomicRanges_1.41.6 GenomeInfoDb_1.25.10
[10] IRanges_2.23.10 S4Vectors_0.27.12 BiocGenerics_0.35.4
loaded via a namespace (and not attached):
[1] reticulate_1.16 tidyselect_1.1.0 fftw_1.0-6
[4] htmlwidgets_1.5.1 grid_4.0.2 BiocParallel_1.23.2
[7] Rtsne_0.15 devtools_2.3.1 munsell_0.5.0
[10] codetools_0.2-16 ica_1.0-2 future_1.18.0
[13] miniUI_0.1.1.1 withr_2.2.0 colorspace_1.4-1
[16] rstudioapi_0.11 Seurat_3.2.0 ROCR_1.0-11
[19] tensor_1.5 listenv_0.8.0 emmeans_1.4.8
[22] GenomeInfoDbData_1.2.3 polyclip_1.10-0 bit64_4.0.2
[25] rprojroot_1.3-2 coda_0.19-3 vctrs_0.3.2
[28] generics_0.0.2 TH.data_1.0-10 R6_2.4.1
[31] ggbeeswarm_0.6.0 clue_0.3-57 rsvd_1.0.3
[34] hdf5r_1.3.2 bitops_1.0-6 spatstat.utils_1.17-0
[37] assertthat_0.2.1 promises_1.1.1 scales_1.1.1
[40] multcomp_1.4-13 beeswarm_0.2.3 gtable_0.3.0
[43] globals_0.12.5 processx_3.4.3 goftest_1.2-2
[46] sandwich_2.5-1 rlang_0.4.7 GlobalOptions_0.1.2
[49] splines_4.0.2 lazyeval_0.2.2 BiocManager_1.30.10
[52] yaml_2.2.1 reshape2_1.4.4 abind_1.4-5
[55] backports_1.1.8 httpuv_1.5.4 tools_4.0.2
[58] usethis_1.6.1 ggplot2_3.3.2 qusage_2.23.0
[61] ellipsis_0.3.1 gplots_3.0.4 RColorBrewer_1.1-2
[64] sessioninfo_1.1.1 ggridges_0.5.2 Rcpp_1.0.5
[67] plyr_1.8.6 progress_1.2.2 zlibbioc_1.35.0
[70] purrr_0.3.4 RCurl_1.98-1.2 ps_1.3.4
[73] prettyunits_1.1.1 rpart_4.1-15 deldir_0.1-28
[76] pbapply_1.4-2 GetoptLong_1.0.2 viridis_0.5.1
[79] cowplot_1.0.0 zoo_1.8-8 ggrepel_0.8.2
[82] cluster_2.1.0 fs_1.5.0 magrittr_1.5
[85] data.table_1.13.0 circlize_0.4.10 lmtest_0.9-37
[88] RANN_2.6.1 mvtnorm_1.1-1 fitdistrplus_1.1-1
[91] pkgload_1.1.0 hms_0.5.3 patchwork_1.0.1
[94] mime_0.9 xtable_1.8-4 gridExtra_2.3
[97] shape_1.4.4 testthat_2.3.2 compiler_4.0.2
[100] scater_1.17.4 tibble_3.0.3 KernSmooth_2.23-17
[103] crayon_1.3.4 R.oo_1.23.0 htmltools_0.5.0
[106] mgcv_1.8-31 later_1.1.0.1 tidyr_1.1.1
[109] ComplexHeatmap_2.5.5 MASS_7.3-51.6 cli_2.0.2
[112] R.methodsS3_1.8.0 gdata_2.18.0 igraph_1.2.5
[115] pkgconfig_2.0.3 plotly_4.9.2.1 scuttle_0.99.12
[118] vipor_0.4.5 XVector_0.29.3 estimability_1.3
[121] stringr_1.4.0 callr_3.4.3 digest_0.6.25
[124] sctransform_0.2.1 RcppAnnoy_0.0.16 spatstat.data_1.4-3
[127] leiden_0.3.3 uwot_0.1.8 DelayedMatrixStats_1.11.1
[130] shiny_1.5.0 gtools_3.8.2 rjson_0.2.20
[133] lifecycle_0.2.0 nlme_3.1-148 jsonlite_1.7.0
[136] BiocNeighbors_1.7.0 desc_1.2.0 viridisLite_0.3.0
[139] limma_3.45.10 fansi_0.4.1 pillar_1.4.6
[142] lattice_0.20-41 fastmap_1.0.1 httr_1.4.2
[145] pkgbuild_1.1.0 survival_3.2-3 glue_1.4.1
[148] remotes_2.2.0 spatstat_1.64-1 png_0.1-7
[151] bit_4.0.4 stringi_1.4.6 BiocSingular_1.5.0
[154] caTools_1.18.0 memoise_1.1.0 dplyr_1.0.1
[157] irlba_2.3.3 future.apply_1.6.0 ape_5.4-1
thanks
conditionterm is namedconditionMCTP39, is that what you expect? You can figure out what all the coefficients are named bycolnames(coef(zlmCond, 'D')).traceback()say right after you get the error, and what is yoursessionInfo()?The name is actually correct, I manually changed it to TREAT just for the sake of this post, to make it easier to understand that it was the treatment group .
traceback()andsessionInfo()are above tnxI am unable to replicate (R 4.0.2, MAST_1.15.0, macOS Mojave 10.14.6). See below for a working example. Can you provide a reproducible example.