DESeq Error (nbinomTest ())
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canfield ▴ 10
@canfield-23654
Last seen 15 months ago

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
Deseq nbinomTest • 229 views
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Entering edit mode

Any reason you use a deprecated package rather than the recommended DESeq2?

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Entering edit mode
canfield ▴ 10
@canfield-23654
Last seen 15 months ago

Possibly solved. My data frame w/ conditions also had a second column with an invariable factor. When I passed the following argument:

cds <- newCountDataSet(deseq.data, rad.design[,"condition"])

...the issue seemed to go away. Hope this might help someone else in the future!

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