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Hi, I cannot resolve the source of this error when I attempt to merge samples using phyloseq. The command is:
> phymerge <- merge_samples(physeq, "expvar")
Error in `rownames<-`(`*tmp*`, value = c("PBRC_LR_BM4218", "PBRC_LR_BM4787", :
attempt to set 'rownames' on an object with no dimensions
I downloaded the Global Patterns example and performed the command successfully with the example dataset. Here is a snapshot of my data.
Thanks for taking a look,
Susan
> head(otu_table(physeq))
OTU Table: [6 taxa and 4 samples]
taxa are rows
PBRC_LR_BM4218 PBRC_LR_BM4787 PBRC_LR_BM8329 PBRC_LR_BM9418
OTU_43 61 10 10 18
OTU_65 11 5 6 3
OTU_110 6 0 0 1
OTU_85 0 0 0 13
OTU_15 5 1 11 1438
OTU_51 16 3 3 15
Taxonomy Table: [6 taxa by 6 taxonomic ranks]:
Domain Phylum Class Order Family
OTU_43 "Bacteria" "Actinobacteria" "Actinobacteria" "Coriobacteridae" "Coriobacteriales"
OTU_65 "Bacteria" "Firmicutes" "Bacilli" "Lactobacillales" "Streptococcaceae"
OTU_110 "Bacteria" "Actinobacteria" "Actinobacteria" "Coriobacteridae" "Coriobacteriales"
OTU_85 "Bacteria" "Proteobacteria" "Alphaproteobacteria" "Caulobacterales" "Caulobacteraceae"
OTU_15 "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pseudomonadales" "Moraxellaceae"
OTU_51 "Bacteria" "Actinobacteria" "Actinobacteria" "Coriobacteridae" "Coriobacteriales"
Genus
OTU_43 "Coriobacterineae"
OTU_65 "Streptococcus"
OTU_110 "Coriobacterineae"
OTU_85 "Brevundimonas"
OTU_15 "Acinetobacter"
OTU_51 "Coriobacterineae"
head(sample_data(physeq))
Sample Data: [4 samples by 1 sample variables]:
expvar
PBRC_LR_BM4218 A
PBRC_LR_BM4787 A
PBRC_LR_BM8329 B
PBRC_LR_BM9418 B
x<- as.data.frame(sample_data(physeq))
> str(x)
'data.frame': 4 obs. of 1 variable:
Formal class 'sample_data' [package "phyloseq"] with 4 slots
..@ .Data :List of 1
.. ..$ : Factor w/ 2 levels "A","B": 1 1 2 2
..@ names : chr "expvar"
..@ row.names: chr "PBRC_LR_BM4218" "PBRC_LR_BM4787" "PBRC_LR_BM8329" "PBRC_LR_BM9418"
..@ .S3Class : chr "data.frame"
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] DESeq2_1.12.2 SummarizedExperiment_1.2.2 Biobase_2.32.0
[4] GenomicRanges_1.24.2 GenomeInfoDb_1.8.2 IRanges_2.6.0
[7] S4Vectors_0.10.1 BiocGenerics_0.18.0 shiny_0.13.2
[10] vegan_2.4-0 lattice_0.20-33 permute_0.9-0
[13] tidyr_0.5.1 doParallel_1.0.10 iterators_1.0.8
[16] foreach_1.4.3 dplyr_0.5.0 plyr_1.8.4
[19] scales_0.4.0 ggplot2_2.1.0 ape_3.5
[22] phyloseq_1.16.2
loaded via a namespace (and not attached):
[1] jsonlite_1.0 splines_3.3.1 Formula_1.2-1 assertthat_0.1
[5] latticeExtra_0.6-28 yaml_2.1.13 RSQLite_1.0.0 chron_2.3-47
[9] digest_0.6.9 RColorBrewer_1.1-2 XVector_0.12.0 colorspace_1.2-6
[13] htmltools_0.3.5 httpuv_1.3.3 Matrix_1.2-6 XML_3.98-1.4
[17] genefilter_1.54.2 zlibbioc_1.18.0 xtable_1.8-2 BiocParallel_1.6.2
[21] tibble_1.1 annotate_1.50.0 mgcv_1.8-12 nnet_7.3-12
[25] survival_2.39-4 magrittr_1.5 mime_0.5 nlme_3.1-128
[29] MASS_7.3-45 foreign_0.8-66 tools_3.3.1 data.table_1.9.6
[33] formatR_1.4 stringr_1.0.0 munsell_0.4.3 locfit_1.5-9.1
[37] cluster_2.0.4 AnnotationDbi_1.34.3 Biostrings_2.40.1 ade4_1.7-4
[41] rhdf5_2.16.0 biomformat_1.0.2 igraph_1.0.1 gtable_0.2.0
[45] codetools_0.2-14 multtest_2.28.0 DBI_0.4-1 reshape2_1.4.1
[49] R6_2.1.2 gridExtra_2.2.1 knitr_1.13 Hmisc_3.17-4
[53] stringi_1.1.1 Rcpp_0.12.5 geneplotter_1.50.0 rpart_4.1-10
[57] acepack_1.3-3.3
Update: I ran the command using a larger number of samples. Problem solved.