SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
MiSeq gDNA reads still fail "Kmer content" and "per base seq content" after trimming" ysnapus Illumina/Solexa 4 11-12-2014 08:25 AM
DEXSeq error in estimateDispersions: match.arg(start.method, c("log(y)", "mean")) fpadilla Bioinformatics 14 07-03-2013 03:11 PM
[DESeq] invalid class "CountDataSet" object Azazel Bioinformatics 4 11-08-2011 01:34 AM
The position file formats ".clocs" and "_pos.txt"? Ist there any difference? elgor Illumina/Solexa 0 06-27-2011 08:55 AM
"Systems biology and administration" & "Genome generation: no engineering allowed" seb567 Bioinformatics 0 05-25-2010 01:19 PM

Reply
 
Thread Tools
Old 10-17-2016, 07:07 PM   #1
SuzuBell
Member
 
Location: Iowa

Join Date: Nov 2013
Posts: 11
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([email protected]) :
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!
SuzuBell is offline   Reply With Quote
Old 10-18-2016, 12:00 AM   #2
Dario1984
Senior Member
 
Location: Sydney, Australia

Join Date: Jun 2011
Posts: 147
Default

That simply means that SummarizedExperiment had its definition changed recently and your variable doesn't have the new slot because it was created before the new definition was in existence. You can use updateObject to easily make your variable conform to the latest definition.
Dario1984 is offline   Reply With Quote
Reply

Tags
edaseq, edger, elementmetadata, summarizedexperiment

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:23 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO