Error in taxa_are_rows(x) : trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
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@jaibersolanoi-23797
Last seen 2.1 years ago

Hi,

I'm trying to use a variance stabilizing transformation with varianceStabilizingTransformation function including in DESeq (I'm using the 1.26.0 version) to get the Euclidean distances and plot a hierarchical clustering of my localities. But, when I used this function I get the following error message:

Error in taxaarerows(x) : trying to get slot "taxaarerows" from an object (class "otu_table") that is not an S4 object

Above, I'll write step by step scripting. I can't understand why I get this error, I was reading about that and I can't similar errors from this function or DESeq function.

Thanks in advance.

To import my biom file, i used:

biom.full <- import_biom(BIOMfilename = "myFile.biom") ## phyloseq 1.30.0

str(biom.full)

Formal class 'phyloseq' [package "phyloseq"] with 5 slots
  ..@ otu_table:Formal class 'otu_table' [package "phyloseq"] with 2 slots
  .. .. ..@ .Data        : num [1:9182, 1:203] 10 0 0 6 0 61 41 0 138 65 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:9182] "4479946" "4479944" "1050608" "973124" ...
  .. .. .. .. ..$ : chr [1:203] "154" "160" "155" "19" ...
  .. .. ..@ taxa_are_rows: logi TRUE
  ..@ tax_table:Formal class 'taxonomyTable' [package "phyloseq"] with 1 slot
  .. .. ..@ .Data: chr [1:9182, 1:7] "k__Bacteria" "k__Bacteria" "k__Bacteria" "k__Bacteria" ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:9182] "4479946" "4479944" "1050608" "973124" ...
  .. .. .. .. ..$ : chr [1:7] "Rank1" "Rank2" "Rank3" "Rank4" ...
  ..@ sam_data : NULL
  ..@ phy_tree : NULL
  ..@ refseq   : NULL

counttab <- otutable(biom.full, errorIfNULL = T)

deseqcounts <- DESeqDataSetFromMatrix(counttab, colData = datos2, design = ~LOCATION)

str(deseq_counts)

deseq_counts

class: DESeqDataSet 
dim: 9182 203 
metadata(1): version
assays(1): counts
rownames(9182): 4479946 4479944 ... New.CleanUp.ReferenceOTU34278 New.CleanUp.ReferenceOTU34449
rowData names(0):
colnames(203): 154 160 ... 101 65
colData names(12): COD N_COD ... ID.QIIME IDtmp

sizeFdeseq <- estimateSizeFactors(deseqcounts, type = "poscounts")

VSTdeseq <- varianceStabilizingTransformation(sizeFdeseq)

Error in taxa_are_rows(x) : 
  trying to get slot "taxa_are_rows" from an object (class "otu_table") that is not an S4 object
#

MY SESSION INFO:

sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] parallel  stats4  stats graphics  grDevices utils datasets  methods base 

other attached packages:
 [1] plotly_4.9.2.1  ggplot2_3.3.2 DESeq2_1.26.0 SummarizedExperiment_1.16.1
 [5] DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0  Biobase_2.46.0 
 [9] GenomicRanges_1.38.0  GenomeInfoDb_1.22.1 IRanges_2.20.2  S4Vectors_0.24.4 
[13] BiocGenerics_0.32.0 phyloseq_1.30.0 xlsx_0.6.3 

loaded via a namespace (and not attached):
 [1] nlme_3.1-148 bitops_1.0-6 bit64_0.9-7  httr_1.4.1 RColorBrewer_1.1-2  
 [6] tools_3.6.3  backports_1.1.8  R6_2.4.1 vegan_2.5-6  rpart_4.1-15  
[11] lazyeval_0.2.2 Hmisc_4.4-0  DBI_1.1.0  mgcv_1.8-31  colorspace_1.4-1  
[16] permute_0.9-5  ade4_1.7-15  nnet_7.3-14  withr_2.2.0  tidyselect_1.1.0  
[21] gridExtra_2.3  bit_1.1-15.2 compiler_3.6.3 htmlTable_2.0.0  scales_1.1.1  
[26] checkmate_2.0.0  genefilter_1.68.0  stringr_1.4.0  digest_0.6.25  foreign_0.8-76  
[31] XVector_0.26.0 base64enc_0.1-3  jpeg_0.1-8.1 pkgconfig_2.0.3  htmltools_0.5.0 
[36] htmlwidgets_1.5.1  rlang_0.4.6  rstudioapi_0.11  RSQLite_2.2.0  generics_0.0.2  
[41] jsonlite_1.7.0 acepack_1.4.1  dplyr_1.0.0  rlist_0.4.6.1  RCurl_1.98-1.2  
[46] magrittr_1.5 GenomeInfoDbData_1.2.2 Formula_1.2-3  biomformat_1.14.0  Matrix_1.2-18 
[51] Rcpp_1.0.4.6 munsell_0.5.0  Rhdf5lib_1.8.0 ape_5.4  lifecycle_0.2.0 
[56] stringi_1.4.6  MASS_7.3-51.6  zlibbioc_1.32.0  rhdf5_2.30.1 plyr_1.8.6  
[61] blob_1.2.1 grid_3.6.3 crayon_1.3.4 lattice_0.20-41  Biostrings_2.54.0 
[66] splines_3.6.3  multtest_2.42.0  annotate_1.64.0  xlsxjars_0.6.1 locfit_1.5-9.4  
[71] knitr_1.29 pillar_1.4.4 igraph_1.2.5 geneplotter_1.64.0 reshape2_1.4.4  
[76] codetools_0.2-16 XML_3.99-0.3 glue_1.4.1 latticeExtra_0.6-29  BiocManager_1.30.10 
[81] data.table_1.12.8  png_0.1-7  vctrs_0.3.1  foreach_1.5.0  tidyr_1.1.0 
[86] gtable_0.3.0 purrr_0.3.4  xfun_0.15  xtable_1.8-4 viridisLite_0.3.0 
[91] survival_3.2-3 tibble_3.0.1 rJava_0.9-12 iterators_1.0.12 memoise_1.1.0 
[96] AnnotationDbi_1.48.0 cluster_2.1.0  ellipsis_0.3.1
deseq2 phyloseq • 567 views
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Entering edit mode
@mikelove
Last seen 21 hours ago
United States

Not sure — otu_table is not a DESeq2 class.

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Entering edit mode

Thanks, I solved my issue.

I got the OTU and taxonomy table (otutable and taxtable, respectively) and exported them as tsv file. So, I read them again each tsv separately with read.table, and build my DESeqDataSet from these.

Now, everything is fine. Thanks.

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