Question: Problem constructing DESeq objects with large integers.
0
gravatar for Zach Brehm
11 days ago by
Zach Brehm0
Zach Brehm0 wrote:

Hello,

I am attempting to construct a dds object out some GTEx data obtained through Recount. When creating the dds object, I am met with an error that I believe is due to integers in the data that are too large for R. I have been unable to find a workaround for this thus far. The following output displays the command that generated the error, the error itself, and my session info.

Thanks, Zach

> dds_merge <- DESeqDataSet(rse_merge, design = ~1) %>% estimateSizeFactors()
converting counts to integer mode
Error in validObject(.Object) : 
  invalid class “DESeqDataSet” object: NA values are not allowed in the count matrix
In addition: Warning message:
In mde(x) : NAs introduced by coercion to integer range
> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.4.0               stringr_1.4.0               dplyr_0.8.0.1              
 [4] purrr_0.3.2                 readr_1.3.1                 tidyr_0.8.3                
 [7] tibble_2.1.1                ggplot2_3.1.1               tidyverse_1.2.1            
[10] DESeq2_1.24.0               SummarizedExperiment_1.14.0 DelayedArray_0.10.0        
[13] BiocParallel_1.17.18        matrixStats_0.54.0          Biobase_2.44.0             
[16] GenomicRanges_1.36.0        GenomeInfoDb_1.20.0         IRanges_2.18.0             
[19] S4Vectors_0.22.0            BiocGenerics_0.30.0        

loaded via a namespace (and not attached):
 [1] nlme_3.1-139           bitops_1.0-6           lubridate_1.7.4        bit64_0.9-7           
 [5] RColorBrewer_1.1-2     httr_1.4.0             tools_3.6.0            backports_1.1.4       
 [9] R6_2.4.0               rpart_4.1-15           Hmisc_4.2-0            DBI_1.0.0             
[13] lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-12            withr_2.1.2           
[17] tidyselect_0.2.5       gridExtra_2.3          bit_1.1-14             compiler_3.6.0        
[21] cli_1.1.0              rvest_0.3.3            htmlTable_1.13.1       xml2_1.2.0            
[25] scales_1.0.0           checkmate_1.9.3        genefilter_1.66.0      digest_0.6.18         
[29] foreign_0.8-71         XVector_0.24.0         base64enc_0.1-3        pkgconfig_2.0.2       
[33] htmltools_0.3.6        htmlwidgets_1.3        rlang_0.3.4            readxl_1.3.1          
[37] rstudioapi_0.10        RSQLite_2.1.1          generics_0.0.2         jsonlite_1.6          
[41] acepack_1.4.1          RCurl_1.95-4.12        magrittr_1.5           GenomeInfoDbData_1.2.1
[45] Formula_1.2-3          Matrix_1.2-17          Rcpp_1.0.1             munsell_0.5.0         
[49] stringi_1.4.3          zlibbioc_1.30.0        plyr_1.8.4             grid_3.6.0            
[53] blob_1.1.1             crayon_1.3.4           lattice_0.20-38        haven_2.1.0           
[57] splines_3.6.0          annotate_1.62.0        hms_0.4.2              locfit_1.5-9.1        
[61] knitr_1.22             pillar_1.4.0           geneplotter_1.62.0     XML_3.98-1.19         
[65] glue_1.3.1             latticeExtra_0.6-28    data.table_1.12.2      modelr_0.1.4          
[69] cellranger_1.1.0       gtable_0.3.0           assertthat_0.2.1       xfun_0.7              
[73] xtable_1.8-4           broom_0.5.2            survival_2.44-1.1      AnnotationDbi_1.46.0  
[77] memoise_1.1.0          cluster_2.0.8         
deseq2 recount • 61 views
ADD COMMENTlink modified 11 days ago • written 11 days ago by Zach Brehm0
Answer: Problem constructing DESeq objects with large integers.
0
gravatar for Michael Love
11 days ago by
Michael Love23k
United States
Michael Love23k wrote:

Are you sure that you don't have an NA in the counts?

You can use anyis.na(...)) on the counts assay for example to test this yourself.

ADD COMMENTlink written 11 days ago by Michael Love23k

Yes, but to be safe I just double checked them with the following:

> max(assay(rse_merge)) - .Machine$integer.max
[1] 13994598706
> anyis.na(assay(rse_merge)))
[1] FALSE
ADD REPLYlink written 11 days ago by Zach Brehm0

Maybe you can follow up with the creators of the object as to why there is a seemingly erroneous value in the assay.

ADD REPLYlink written 11 days ago by Michael Love23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 120 users visited in the last hour