Question: calculateRPKM error in customProDB
0
gravatar for javamng
21 months ago by
javamng0
javamng0 wrote:

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.

 

software error customprodb • 596 views
ADD COMMENTlink modified 13 months ago by georges.bedran0 • written 21 months ago by javamng0
Answer: calculateRPKM error in customProDB
0
gravatar for georges.bedran
13 months ago by
georges.bedran0 wrote:

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.

 

ADD COMMENTlink written 13 months ago by georges.bedran0

Hello,

I am experiencing the same problem

> anno <- keepSeqlevels(anno, seqlevels(galn))
Error in keepSeqlevels(anno, seqlevels(galn)) : 
  invalid seqlevels: JH584301.1, JH584300.1, JH584302.1, GL456379.1, GL456393.1, GL456366.1, GL456367.1, GL456213.1,
  GL456383.1, GL456360.1, GL456378.1, GL456389.1, GL456370.1, GL456387.1, GL456390.1, GL456394.1, GL456392.1, GL456382.1,
  GL456359.1, GL456396.1, GL456368.1

Even with your suggestion it is still giving an error

> anno <- keepSeqlevels(anno,seqlevels(galn), pruning.mode="coarse")
Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : 
  invalid seqlevels: JH584301.1, JH584300.1, JH584302.1, GL456379.1, GL456393.1, GL456366.1, GL456367.1, GL456213.1,
  GL456383.1, GL456360.1, GL456378.1, GL456389.1, GL456370.1, GL456387.1, GL456390.1, GL456394.1, GL456392.1, GL456382.1,
  GL456359.1, GL456396.1, GL456368.1

 

Any idea how to fix this?

ADD REPLYlink written 5 months ago by piero.giansanti0
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