Question

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function assayNames for signature "DESeqDataSet"

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nooshin ▴ 300

@nooshin-5239

Last seen 5.4 years ago

Hi,

I want to use DESeq2 to find deferentially expressed genes under specific condition, however it produces strange error:

> dds <- DESeqDataSetFromMatrix(countData = counts,colData = colData,design = ~ condition + time)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘assayNames’ for signature ‘"DESeqDataSet"’

I would appreciate your help a lot.

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

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] DESeq2_1.10.1              RcppArmadillo_0.7.100.3.1  Rcpp_0.12.5                SummarizedExperiment_1.2.2
 [5] Biobase_2.30.0             GenomicRanges_1.25.0       GenomeInfoDb_1.6.3         IRanges_2.7.1             
 [9] S4Vectors_0.11.2           BiocGenerics_0.19.0        edgeR_3.12.1               limma_3.26.9              
[13] BiocInstaller_1.20.3      

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.4           XVector_0.13.0       futile.options_1.0.0
 [6] tools_3.3.0          zlibbioc_1.16.0      rpart_4.1-10         RSQLite_1.0.0        annotate_1.51.0     
[11] gtable_0.2.0         lattice_0.20-33      Matrix_1.2-6         DBI_0.4-1            gridExtra_2.2.1     
[16] genefilter_1.52.1    cluster_2.0.4        locfit_1.5-9.1       grid_3.3.0           nnet_7.3-12         
[21] data.table_1.9.6     AnnotationDbi_1.35.3 XML_3.98-1.4         survival_2.39-4      BiocParallel_1.4.3  
[26] foreign_0.8-66       latticeExtra_0.6-28  Formula_1.2-1        geneplotter_1.48.0   ggplot2_2.1.0       
[31] lambda.r_1.1.7       Hmisc_3.17-4         scales_0.4.0         splines_3.3.0        xtable_1.8-2        
[36] colorspace_1.2-6     acepack_1.3-3.3      munsell_0.4.3        chron_2.3-47

deseq2 error • 2.9k views

ADD COMMENT • link updated 7.9 years ago by Michael Love 41k • written 7.9 years ago by nooshin ▴ 300

score 0 · Answer 1 · 2016-06-14

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Michael Love 41k

@mikelove

Last seen 10 hours ago

United States

You need to update your Bioconductor packages. You are using DESeq2 v1.10 which is linked to a previous version of R.

See here:

http://bioconductor.org/install

ADD COMMENT • link 7.9 years ago Michael Love 41k

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thanks a lot for your response, but it says that edgeR does not exist for R 3.3 :(

ADD REPLY • link 7.9 years ago nooshin ▴ 300

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You should make a new post about that. That is not the case, just a bug. In the new post, also show your sessionInfo() like you have here, what you typed, and what the error said when you try to install edgeR in a fresh R session.

ADD REPLY • link 7.9 years ago Michael Love 41k

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As with C: DECIPHER version bug using biocLite(), your version of BiocInstaller is not correct for your version of R -- it should say so when you load BiocInstaller, right? Follow these directions for updating BiocInstaller.

ADD REPLY • link 7.9 years ago Martin Morgan 25k

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Thanks a lot for your help. I will follow the instruction and make a new post in case of facing an error.

ADD REPLY • link 7.9 years ago nooshin ▴ 300