Hi, I made a mistake using identical() to compare 2 AAStrings, as in
which returns TRUE. That seems to compare lengths. It took me a while to see I was not getting the result I expected and to learn the correct comparison operator is '=='. Maybe I should have been warned off? Thank you.
sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  Biostrings_2.32.0 XVector_0.4.0 IRanges_1.22.7  BiocGenerics_0.10.0 BiocInstaller_1.14.3 loaded via a namespace (and not attached):  compiler_3.1.1 stats4_3.1.1 tools_3.1.1 zlibbioc_1.10.0