DESeq Error (nbinomTest ())
1
0
Entering edit mode
canfield ▴ 10
@canfield-23654
Last seen 3.8 years 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 • 954 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
canfield ▴ 10
@canfield-23654
Last seen 3.8 years 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!

ADD COMMENT

Login before adding your answer.

Traffic: 835 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6