Hello,

I am trying to create the DESeqDataSetFromMatrix, and am receiving an error that there is an invalid class "summarizedExperiment" object. I initially thought there was something wrong with my input files, but I receive the same errors when I use the Pasilla dataset and enter in all code as outlined in the instructions here (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#quick-start)

I have entered the input and full error below, as well as the sessionInfo().

Thank you for any help with this!

library("DESeq2")

dds <- DESeqDataSetFromMatrix(countData = cts,

                              colData = coldata,

                              design = ~ condition)

dds

Error in validObject(.Object): invalid class “SummarizedExperiment” object: undefined class for slot "NAMES" ("characterORNULL")
Traceback:

1. DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~condition)
2. SummarizedExperiment(assays = SimpleList(counts = countData),
.     colData = colData, ...)
3. SummarizedExperiment(assays = SimpleList(counts = countData),
.     colData = colData, ...)
4. .local(assays, ...)
5. new_SummarizedExperiment(assays, ans_rownames, rowData, colData,
.     metadata)
6. new("SummarizedExperiment", NAMES = names, elementMetadata = rowData,
.     colData = colData, assays = assays, metadata = as.list(metadata))
7. initialize(value, ...)
8. initialize(value, ...)
9. validObject(.Object)
10. stop(msg, ": ", errors, domain = NA)

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /ebio/abt3_projects/Christensenella_Project/anaconda3/envs/R_DEseq2/lib/R/lib/libRblas.so
LAPACK: /ebio/abt3_projects/Christensenella_Project/anaconda3/envs/R_DEseq2/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
 [1] BiocInstaller_1.28.0       BiocParallel_1.12.0       
 [3] DESeq2_1.18.1              SummarizedExperiment_1.4.0
 [5] Biobase_2.38.0             GenomicRanges_1.30.0      
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0            
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0       
[11] ggplot2_2.2.1              tidyr_0.6.3               
[13] dplyr_0.7.0               

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1          Rcpp_0.12.13            lattice_0.20-34        
 [4] assertthat_0.2.0        digest_0.6.12           IRdisplay_0.4.4        
 [7] R6_2.2.1                plyr_1.8.4              repr_0.10              
[10] acepack_1.4.1           RSQLite_1.1-2           evaluate_0.10          
[13] zlibbioc_1.24.0         rlang_0.1.2             lazyeval_0.2.0         
[16] uuid_0.1-2              annotate_1.56.0         rpart_4.1-10           
[19] Matrix_1.2-7.1          splines_3.4.1           geneplotter_1.56.0     
[22] stringr_1.2.0           foreign_0.8-67          RCurl_1.95-4.8         
[25] munsell_0.4.3           compiler_3.4.1          nnet_7.3-12            
[28] tibble_1.3.3            GenomeInfoDbData_0.99.1 Hmisc_3.14-6           
[31] XML_3.98-1.6            crayon_1.3.2            bitops_1.0-6           
[34] grid_3.4.1              jsonlite_1.5            xtable_1.8-2           
[37] gtable_0.2.0            DBI_0.6-1               magrittr_1.5           
[40] scales_0.4.1            stringi_1.1.2           XVector_0.18.0         
[43] genefilter_1.60.0       latticeExtra_0.6-28     IRkernel_0.7.1         
[46] Formula_1.2-1           RColorBrewer_1.1-2      tools_3.4.1            
[49] glue_1.1.1              survival_2.40-1         AnnotationDbi_1.40.0   
[52] colorspace_1.3-2        cluster_2.0.6           memoise_1.1.0          
[55] pbdZMQ_0.2-6 

Usually this is a problem associated with package versions from different Bioconductor releases; what does BiocInstaller::biocValid() say? If it looks clean, I'd suggest re-installing the packages (via biocLite()) SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, XVector.

Can you run biocLite() and update all packages until you get no errors from biocValid()? 

I can see you have an old version of SummarizedExperiment (the current version is 1.8). Bioconductor packages are designed to work all together based on consistent releases.

In the past, this error came up when there were mixed versions of software on the machine:

DESeqDataSetFromTximport: Error in checkSlotAssignment