I recently installed the customProDB package.

And when I run calculateRPKM, I get the following message

Please let me know if you have seen any of these problems.

thanks!

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
[1] customProDB_1.16.0   biomaRt_2.32.1       AnnotationDbi_1.38.2
[4] Biobase_2.36.2       IRanges_2.10.2       S4Vectors_0.14.3
[7] BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               plyr_1.8.4
 [3] compiler_3.4.1             GenomeInfoDb_1.12.2
 [5] XVector_0.16.0             GenomicFeatures_1.28.4
 [7] bitops_1.0-6               tools_3.4.1
 [9] zlibbioc_1.22.0            digest_0.6.12
[11] bit_1.1-12                 AhoCorasickTrie_0.1.0
[13] RSQLite_2.0                memoise_1.1.0
[15] tibble_1.3.3               lattice_0.20-35
[17] BSgenome_1.44.0            rlang_0.1.1
[19] Matrix_1.2-10              DelayedArray_0.2.7
[21] DBI_0.7                    GenomeInfoDbData_0.99.0
[23] stringr_1.2.0              rtracklayer_1.36.4
[25] Biostrings_2.44.2          bit64_0.9-7
[27] grid_3.4.1                 XML_3.98-1.9
[29] BiocParallel_1.10.1        magrittr_1.5
[31] blob_1.1.0                 Rsamtools_1.28.0
[33] matrixStats_0.52.2         GenomicRanges_1.28.4
[35] GenomicAlignments_1.12.1   SummarizedExperiment_1.6.3
[37] stringi_1.1.5              RCurl_1.95-4.8
[39] VariantAnnotation_1.22.3

--------- Error Messages -------

> RPKM <- calculateRPKM(bamFile, exon, proteincodingonly=TRUE, ids)
Error in keepSeqlevels(anno, seqlevels(galn)) :
  invalid seqlevels: KI270729.1, KI270743.1, GL000008.2, KI270747.1,
  KI270722.1, KI270742.1, KI270736.1, GL000224.1, KI270719.1, KI270712.1,
  KI270706.1, KI270725.1, KI270715.1, KI270749.1, KI270741.1, GL000221.1,
  KI270716.1, KI270751.1, KI270519.1, GL000214.1, KI270708.1, KI270730.1,
  KI270438.1, KI270737.1, KI270738.1, KI270748.1, KI270435.1, GL000208.1,
  KI270538.1, KI270756.1, KI270739.1, KI270757.1, KI270709.1, KI270746.1,
  KI270753.1, KI270589.1, KI270735.1, KI270745.1, KI270714.1, KI270732.1,
  KI270754.1, KI270710.1, KI270717.1, KI270724.1, KI270720.1, KI270723.1,
  KI270718.1, KI270317.1, KI270740.1, KI270755.1, KI270707.1, KI270579.1,
  KI270752.1, KI270512.1, KI270322.1, GL000226.1, KI270311.1, KI270366.1,
  KI270511.1, KI270448.1, KI270521.1, KI270581.1, KI270582.1, KI270515.1,
  KI270588.1, KI270591.1, KI270522.1, KI270507.1, KI270590.1, KI270584.1,
  KI270320.1, KI270382.1, KI270468.1, KI270467.1, KI270362.1, KI270517.1,
  KI270593.1, KI270528.1, KI270587.

Hello,

since the last few bioconductor updates the keepSeqlevels functions had the default pruning.mode option changed to raise an erorr in case arg1 and arg2 contain different levels (chromosomes).

You only have to add the argument pruning.mode="coarse" to replicate the old behaviour.

You just have to replace lines 49 and 50 of the calcuteRPKM.R source code file with the following :

            anno <- keepSeqlevels(anno,seqlevels(galn), pruning.mode="coarse")
            galn <- keepSeqlevels(galn,seqlevels(anno), pruning.mode="coarse")

then add the whole modified function "calculateRPKM" to your script before calling it.