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Old 10-17-2016, 06:07 PM   #1
SuzuBell
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Location: U.S.A

Join Date: Nov 2013
Posts: 20
Default no slot of name "elementMetadata" for this object of class "SummarizedExperiment"

I have a count table that was saved as an .rda file. I was always able to open the .rda file in R simply using load("myData.rda"). Recently, upon trying to open the same file, I received an error in R as follows:

Error in nrow(x@elementMetadata) :
no slot of name "elementMetadata" for this object of class "SummarizedExperiment"

Even though this error is output, loading in the data does create the countTable
object in the R session. When I do:

slotNames(countTable)

I get five answers:

[1] "colData" "assays" "NAMES" "elementMetadata" "metadata"

Since that include "elementMetadata" and since I was always able to read in this file, I am confused what may be causing this. My R session information is as follows:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] scales_0.4.0 reshape2_1.4.1 gridExtra_2.2.1
[4] matrixStats_0.51.0 dplyr_0.5.0 EDASeq_2.6.2
[7] ShortRead_1.30.0 BiocParallel_1.6.6 stringr_1.1.0
[10] edgeR_3.14.0 limma_3.28.21 GGally_1.2.0
[13] ggplot2_2.1.0 GenomicAlignments_1.8.4 SummarizedExperiment_1.2.3
[16] Biobase_2.32.0 Rsamtools_1.24.0 Biostrings_2.40.2
[19] XVector_0.12.1 rtracklayer_1.32.2 GenomicRanges_1.24.3
[22] GenomeInfoDb_1.8.7 IRanges_2.6.1 S4Vectors_0.10.3
[25] BiocGenerics_0.18.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 RColorBrewer_1.1-2 plyr_1.8.4 GenomicFeatures_1.24.5
[5] R.methodsS3_1.7.1 bitops_1.0-6 R.utils_2.4.0 tools_3.3.1
[9] zlibbioc_1.18.0 biomaRt_2.28.0 tibble_1.2 RSQLite_1.0.0
[13] annotate_1.50.1 gtable_0.2.0 lattice_0.20-34 Matrix_1.2-7.1
[17] DBI_0.5-1 DESeq_1.24.0 genefilter_1.54.2 hwriter_1.3.2
[21] aroma.light_3.2.0 grid_3.3.1 reshape_0.8.5 R6_2.2.0
[25] AnnotationDbi_1.34.4 survival_2.39-5 XML_3.98-1.4 latticeExtra_0.6-28
[29] geneplotter_1.50.0 magrittr_1.5 splines_3.3.1 assertthat_0.1
[33] xtable_1.8-2 colorspace_1.2-7 stringi_1.1.2 RCurl_1.95-4.8
[37] munsell_0.4.3 R.oo_1.20.0

Any help is greatly appreciated!
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