Hello,
I am trying to follow the example on ALL data set. I ran
filt_bcrneg = nsFilter(ALL_bcrneg, require.entrez=TRUE,
require.GOBP=TRUE, remove.dupEntrez=TRUE,
var.func=IQR, var.cutoff=varCut,
feature.exclude="^AFFX")
And receive this error:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘columns’ for signature ‘"function"’
Here is my session info:
R version 3.2.5 (2016-04-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2_2.2.0 genefilter_1.52.1 ALL_1.12.0 BiocInstaller_1.20.1 GEOquery_2.36.0 Biobase_2.30.0 BiocGenerics_0.16.1
[8] ggplot2_2.1.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.4 AnnotationDbi_1.32.3 splines_3.2.5 IRanges_2.4.8 munsell_0.4.3 lattice_0.20-33 colorspace_1.2-6
[8] xtable_1.8-2 plyr_1.8.3 tools_3.2.5 grid_3.2.5 gtable_0.2.0 DBI_0.4 survival_2.39-2
[15] digest_0.6.9 Matrix_1.2-6 S4Vectors_0.8.11 bitops_1.0-6 rsconnect_0.4.3 RCurl_1.95-4.8 RSQLite_1.0.0
[22] labeling_0.3 scales_0.4.0 stats4_3.2.5 XML_3.98-1.4 annotate_1.48.0
Please advise how I can fix this.
Many thanks,
S.
