Aloha,
I'm trying to work with DESeq and call the nbinomTest() function. When I do, I get the following error message:
Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
missing value where TRUE/FALSE needed
I think my data are formatted correctly. I have a table formatted as described in the manual ("deseq.data"), and created a dataframe ("rad.design") with sample ID, a column for condition ("F" or "M"), and a column for libtype ("single-end"). I then call the following functions:
cds <- newCountDataSet(deseq.data, rad.design)
cds <- estimateSizeFactors(cds)
cds <- estimateDispersions(cds, fitType="local")
res <- nbinomTest(cds, "F", "M")
What does the function expect that is not being provided?
I am a novice when it comes to programming, so please forgive me if this should be an easy/obvious fix!
Many thanks,
Sean
PS: As requested, here's the output of the sessionInfo() command:
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq_1.39.0 lattice_0.20-41 locfit_1.5-9.4 Biobase_2.48.0 BiocGenerics_0.34.0 dplyr_1.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 RColorBrewer_1.1-2 pillar_1.4.4 compiler_4.0.0 BiocManager_1.30.10 bitops_1.0-6
[7] tools_4.0.0 digest_0.6.25 bit_1.1-15.2 annotate_1.66.0 RSQLite_2.2.0 memoise_1.1.0
[13] lifecycle_0.2.0 tibble_3.0.1 pkgconfig_2.0.3 rlang_0.4.6 Matrix_1.2-18 DBI_1.1.0
[19] genefilter_1.70.0 IRanges_2.22.2 S4Vectors_0.26.1 generics_0.0.2 vctrs_0.3.0 stats4_4.0.0
[25] bit64_0.9-7 grid_4.0.0 tidyselect_1.1.0 glue_1.4.1 R6_2.4.1 AnnotationDbi_1.50.0
[31] survival_3.1-12 XML_3.99-0.3 geneplotter_1.66.0 purrr_0.3.4 blob_1.2.1 magrittr_1.5
[37] splines_4.0.0 ellipsis_0.3.1 xtable_1.8-4 RCurl_1.98-1.2 crayon_1.3.4
Any reason you use a deprecated package rather than the recommended DESeq2?