Question: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResults"
0
gravatar for lech.kaczmarczyk
10 weeks ago by
lech.kaczmarczyk10 wrote:

I'm trying to run DESeq2 but got stud on this error:

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
Error in summary.DESeqResults(res) : 
  could not find function "summary.DESeqResults"

The package was fully functional on my computer before. Re-installation of the package did not solve the problem. Session info below.

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] biomaRt_2.41.6              limma_3.41.6                vsn_3.53.0                  data.table_1.12.2          
 [5] dplyr_0.8.3                 ggrepel_0.8.1               ggplot2_3.2.0               PoiClaClu_1.0.2.1          
 [9] RColorBrewer_1.1-2          pheatmap_1.0.12             DESeq2_1.25.5               SummarizedExperiment_1.15.5
[13] DelayedArray_0.11.4         BiocParallel_1.19.0         matrixStats_0.54.0          Biobase_2.45.0             
[17] GenomicRanges_1.37.14       GenomeInfoDb_1.21.1         IRanges_2.19.10             S4Vectors_0.23.17          
[21] BiocGenerics_0.31.5        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6             bit64_0.9-7              progress_1.2.2           httr_1.4.0               tools_3.6.0             
 [6] backports_1.1.4          affyio_1.55.0            R6_2.4.0                 rpart_4.1-15             Hmisc_4.2-0             
[11] DBI_1.0.0                lazyeval_0.2.2           colorspace_1.4-1         nnet_7.3-12              withr_2.1.2             
[16] tidyselect_0.2.5         gridExtra_2.3            prettyunits_1.0.2        preprocessCore_1.47.1    bit_1.1-14              
[21] curl_3.3                 compiler_3.6.0           htmlTable_1.13.1         labeling_0.3             rtracklayer_1.45.1      
[26] scales_1.0.0             checkmate_1.9.4          hexbin_1.27.3            affy_1.63.0              genefilter_1.67.1       
[31] askpass_1.1              rappdirs_0.3.1           stringr_1.4.0            digest_0.6.20            Rsamtools_2.1.2         
[36] foreign_0.8-71           XVector_0.25.0           base64enc_0.1-3          pkgconfig_2.0.2          htmltools_0.3.6         
[41] dbplyr_1.4.2             htmlwidgets_1.3          rlang_0.4.0              rstudioapi_0.10          RSQLite_2.1.1           
[46] acepack_1.4.1            RCurl_1.95-4.12          magrittr_1.5             GenomeInfoDbData_1.2.1   Formula_1.2-3           
[51] Matrix_1.2-17            Rcpp_1.0.1               munsell_0.5.0            stringi_1.4.3            zlibbioc_1.31.0         
[56] BiocFileCache_1.9.1      grid_3.6.0               blob_1.1.1               crayon_1.3.4             lattice_0.20-38         
[61] Biostrings_2.53.1        splines_3.6.0            GenomicFeatures_1.37.3   annotate_1.63.0          hms_0.4.2               
[66] locfit_1.5-9.1           knitr_1.23               pillar_1.4.2             geneplotter_1.63.0       XML_3.98-1.20           
[71] glue_1.3.1               latticeExtra_0.6-28      BiocManager_1.30.4       gtable_0.3.0             openssl_1.4             
[76] purrr_0.3.2              assertthat_0.2.1         xfun_0.8                 xtable_1.8-4             survival_2.44-1.1       
[81] tibble_2.1.3             GenomicAlignments_1.21.4 AnnotationDbi_1.47.0     memoise_1.1.0            cluster_2.1.0
deseq2 • 115 views
ADD COMMENTlink modified 10 weeks ago by Michael Love25k • written 10 weeks ago by lech.kaczmarczyk10
Answer: Error in summary.DESeqResults(res) : could not find function "summary.DESeqResu
2
gravatar for Michael Love
10 weeks ago by
Michael Love25k
United States
Michael Love25k wrote:

Recently, I had to change the way summary() works in DESeq2, moving it from a S3 to an S4 method, because of changes to the underlying class of DESeqResults.

Can you run:

BiocManager::valid()

?

Note that with a complete set of devel packages, DESeq2 builds (including summary() calls in the vignette) on all platforms:

http://bioconductor.org/checkResults/devel/bioc-LATEST/DESeq2/

ADD COMMENTlink written 10 weeks ago by Michael Love25k
> BiocManager::valid("DESeq2") 
[1] TRUE

Should I install it some other way than with BiocManager()?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by lech.kaczmarczyk10

Tried to install it from source, but it did not solve the problem...

ADD REPLYlink written 10 weeks ago by lech.kaczmarczyk10

Another try, can you post your code? You didn’t post code, just messages and errors.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Michael Love25k
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