phyloseq merge_samples attempt to set rownames on an object with no dimensions
0
0
Entering edit mode
newmanss • 0
@newmanss-7190
Last seen 3.7 years ago
United States

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     

 

phyloseq merge_samples rownames error • 1.3k views
ADD COMMENT
0
Entering edit mode

Update:  I ran the command using a larger number of samples.  Problem solved.

ADD REPLY

Login before adding your answer.

Traffic: 496 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6