Search
Question: DESeq2: error with DESeqDataSet function
0
gravatar for Elias Ruiz
16 days 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 16 days ago by Michael Love14k • written 16 days ago by Elias Ruiz0
0
gravatar for Michael Love
16 days ago by
Michael Love14k
United States
Michael Love14k 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 16 days ago by Michael Love14k
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 2.2.0
Traffic: 308 users visited in the last hour