Hi, 

I tried writing to the pData slot of my LumiBatch object (read in using lumiR), this afternoon and got the following error.

> pData(raw_data)       <- pheno_table
Error in (function (classes, fdef, mtable)  : unable to find an inherited method for function ‘pData<-’ for signature ‘"LumiBatch", "tbl_df"’

I've used this function before and haven't had any problems. - I was wondering if other people are experiencing this issue?  

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readr_0.1.1          lumi_2.20.1          Biobase_2.28.0       BiocGenerics_0.14.0 
[5] BiocInstaller_1.18.3

loaded via a namespace (and not attached):
 [1] mclust_5.0.1            base64_1.1              Rcpp_0.11.6            
 [4] locfit_1.5-9.1          lattice_0.20-31         nleqslv_2.8            
 [7] Rsamtools_1.20.4        Biostrings_2.36.1       digest_0.6.8           
[10] foreach_1.4.2           GenomeInfoDb_1.4.1      plyr_1.8.3             
[13] futile.options_1.0.0    stats4_3.2.1            RSQLite_1.0.0          
[16] bumphunter_1.8.0        zlibbioc_1.14.0         GenomicFeatures_1.20.1 
[19] annotate_1.46.0         S4Vectors_0.6.1         Matrix_1.2-1           
[22] preprocessCore_1.30.0   splines_3.2.1           BiocParallel_1.2.6     
[25] stringr_1.0.0           RCurl_1.95-4.7          biomaRt_2.24.0         
[28] rtracklayer_1.28.5      multtest_2.24.0         pkgmaker_0.22          
[31] mgcv_1.8-6              GEOquery_2.34.0         quadprog_1.5-5         
[34] IRanges_2.2.5           codetools_0.2-11        matrixStats_0.14.2     
[37] XML_3.98-1.3            reshape_0.8.5           GenomicAlignments_1.4.1
[40] MASS_7.3-41             bitops_1.0-6            grid_3.2.1             
[43] affy_1.46.1             nlme_3.1-120            xtable_1.7-4           
[46] registry_0.2            DBI_0.3.1               magrittr_1.5           
[49] KernSmooth_2.23-14      stringi_0.5-5           XVector_0.8.0          
[52] genefilter_1.50.0       affyio_1.36.0           doRNG_1.6              
[55] limma_3.24.12           minfi_1.14.0            futile.logger_1.4.1    
[58] nor1mix_1.2-0           lambda.r_1.1.7          RColorBrewer_1.1-2     
[61] iterators_1.0.7         siggenes_1.42.0         tools_3.2.1            
[64] illuminaio_0.10.0       rngtools_1.2.4          survival_2.38-2        
[67] methylumi_2.14.0        AnnotationDbi_1.30.1    colorspace_1.2-6       
[70] GenomicRanges_1.20.5    beanplot_1.2           

Neat. At some point in your work flow you've coerced your plain-old data.frame into a tbl_df, probably indirectly but you could have done it like

library(Biobase)
library(dplyr)
data(sample.ExpressionSet)
eset = sample.ExpressionSet
tbl_df(pData(eset))

Assignment for the data.frame works but not for the new-fangled object

> pData(eset) = pData(eset)
> pData(eset) = tbl_df(pData(eset))
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'pData<-' for signature '"ExpressionSet", "tbl_df"'

The reason is that ExpressionSet doesn't know that the 'tbl_df' class extends data.frame (maybe it should be able to figure this out: 

> class(tbl_df(pData(eset)))
[1] "tbl_df"     "tbl"        "data.frame"

The solution is to coerce your new-fangled object to a data.frame

> pData(eset) = as.data.frame(tbl_df(pData(eset)))
>