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Question: DESeq2: error with DESeqDataSet function
0
gravatar for Elias Ruiz
11 weeks ago by
Elias Ruiz0
Mexico. UNAM.
Elias Ruiz0 wrote:

Please Help!

Hello, since the early September's release of DESeq2 and other libraries , I can not run the function DESeqDataSet, I get the error:

 

dds <- DESeqDataSet(se, design = ~ hour) #DESeqDataSet object

Error in checkSlotAssignment(object, name, value) : 

assignment of an object of class “NULL” is not valid for slot ‘NAMES’ in an object of class “DESeqDataSet”; is(value, "characterORNULL") is not TRUE

 

I already tried re-installing DESeq2 and other packages.

 

sessionInfo()                                                                                      R version 3.4.1 (2017-06-30)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

 

Matrix products: default

BLAS: /export/apps/bioconda/lib/R/lib/libRblas.so

LAPACK: /export/apps/bioconda/lib/R/lib/libRlapack.so

 

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 

attached base packages:

[1] stats4    parallel  stats     graphics  grDevices utils     datasets

[8] methods   base

 

other attached packages:

 [1] DESeq2_1.16.1              BiocInstaller_1.26.1

 [3] biomaRt_2.32.1             BiocParallel_1.10.1

 [5] GenomicAlignments_1.12.2   SummarizedExperiment_1.6.5

 [7] DelayedArray_0.2.7         matrixStats_0.52.2

 [9] GenomicFeatures_1.28.5     AnnotationDbi_1.38.2

[11] Biobase_2.36.2             Rsamtools_1.28.0

[13] Biostrings_2.44.2          XVector_0.16.0

[15] GenomicRanges_1.28.6       GenomeInfoDb_1.12.3

[17] IRanges_2.10.5             S4Vectors_0.14.7

[19] BiocGenerics_0.22.1

 

loaded via a namespace (and not attached):

 [1] locfit_1.5-9.1          Rcpp_0.12.13            lattice_0.20-35

 [4] digest_0.6.12           plyr_1.8.4              backports_1.1.1

 [7] acepack_1.4.1           RSQLite_2.0             ggplot2_2.2.1

[10] zlibbioc_1.22.0         rlang_0.1.2             lazyeval_0.2.0

[13] data.table_1.10.4-1     annotate_1.54.0         blob_1.1.0

[16] rpart_4.1-11            Matrix_1.2-11           checkmate_1.8.4

[19] splines_3.4.1           geneplotter_1.54.0      stringr_1.2.0

[22] foreign_0.8-69          htmlwidgets_0.9         RCurl_1.95-4.8

[25] bit_1.1-12              munsell_0.4.3           compiler_3.4.1

[28] rtracklayer_1.36.5      pkgconfig_2.0.1         base64enc_0.1-3

[31] htmltools_0.3.6         nnet_7.3-12             tibble_1.3.4

[34] gridExtra_2.3           htmlTable_1.9           GenomeInfoDbData_0.99.0

[37] Hmisc_4.0-3             XML_3.98-1.7            bitops_1.0-6

[40] grid_3.4.1              xtable_1.8-2            gtable_0.2.0

[43] DBI_0.7                 magrittr_1.5            scales_0.5.0

[46] stringi_1.1.5           genefilter_1.58.1       latticeExtra_0.6-28

[49] Formula_1.2-2           RColorBrewer_1.1-2      tools_3.4.1

[52] bit64_0.9-7             survival_2.41-3         colorspace_1.3-2

[55] cluster_2.0.6           memoise_1.1.0           knitr_1.17

 

ADD COMMENTlink modified 11 weeks ago by Michael Love15k • written 11 weeks ago by Elias Ruiz0
0
gravatar for Michael Love
11 weeks ago by
Michael Love15k
United States
Michael Love15k wrote:

Can you run biocLite() to make sure everything is up to date and then

se <- updateObject(se)

This was the solution when it came up earlier on the support site, for example

Error creating DESeqDataSet from "airway" SummarizedExperiment

ADD COMMENTlink written 11 weeks ago by Michael Love15k
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