Hi,

I've been using the differential splicing functions within limma as outlined in the user guide. I've updated to the newest version of limma today and it looks like the functions topSplice() and plotSplice() have now been removed from the package (within diffSplice.R) 

> library(limma)

> topSplice()
Error in topSplice() : could not find function "topSplice"

> plotSplice()
Error in plotSplice() : could not find function "plotSplice"

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.0
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
[1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8     
[8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] limma_3.32.8

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2  

I see in the change log that some bug fixes were performed for plotSplice(), however, it looks as if they have been removed in version 3.32.8 compared to version 3.32.7. I'm assuming that this was not intentional?

Best,

Gareth

Yes. According to the git log, there were some changes made between 3.32.7 and 3.32.8 that didn't all make it into 3.32.8. But they are all in 3.32.9, which hasn't been built yet. It should appear within the next 24 hours or so.