Search
Question: (Closed) error in analyzeAlternativeSplicing or analyzeIntronRetention, IsoformSwitchAnalyzeR
0
gravatar for Ou, Jianhong
12 days ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi Kristoffer Vitting-Seerup,

I am trying to use IsoformSwitchAnalyzeR to analyze my RNAseq data. When I trying to run analyzeAlternativeSplicing, I got error:

Error in `[.data.frame`(localExonSkippingIndex, 1) : 
  undefined columns selected

Is there any thing I missed?

Here is my code:

library(IsoformSwitchAnalyzeR)
aSwitchList <- importRdata(
 isoformCountMatrix = counts,
 isoformRepExpression = exp,
 designMatrix = data.frame(sampleID=colnames(counts)[-1], condition=sub("_rep.", "", colnames(counts)[-1])),
 isoformExonAnnoation = localAnnotation)

aSwitchList <- preFilter(aSwitchList, geneExpressionCutoff = 1, isoformExpressionCutoff = 0, removeSingleIsoformGenes = TRUE)
aSwitchList <- isoformSwitchTestDRIMSeq( aSwitchList )
library(BSgenome.Drerio.UCSC.danRer10)
exampleSwitchListAnalyzed <- analyzeORF( aSwitchList, genomeObject= Drerio)
exampleSwitchListAnalyzed <- analyzeAlternativeSplicing( exampleSwitchListAnalyzed )

Here is the data:

counts table:
                             isoform_id   inj_rep1   inj_rep2   uni_rep1    uni_rep2
ENSDART00000097631.4 ENSDART00000097631   49.91803   52.16553   76.69467   78.242030
ENSDART00000169443.1 ENSDART00000169443  187.08195  223.83441  196.30529  151.757982
ENSDART00000170158.1 ENSDART00000170158  394.17787  397.74052    0.00000    5.638381
ENSDART00000171794.2 ENSDART00000171794  372.23452  477.79328  275.56682  260.489120
ENSDART00000164713.1 ENSDART00000164713  448.81833  432.34869 2118.43899 2272.995210
ENSDART00000168732.1 ENSDART00000168732 1332.93794 1253.32564 6279.55023 5764.982906
ENSDART00000167905.1 ENSDART00000167905 1332.93794 1253.32564 3329.92554 4071.962573
ENSDART00000170411.1 ENSDART00000170411  179.87738  196.09420  139.91539  137.285373
ENSDART00000169846.1 ENSDART00000169846  471.68002  418.38313  104.52679   77.551425
ENSDART00000169539.1 ENSDART00000169539  228.64206  303.15667  116.05971  116.691904
ENSDART00000168709.1 ENSDART00000168709  170.52131  215.26682   39.42153   35.757866
ENSDART00000167456.1 ENSDART00000167456   71.67936   37.00505   44.85629   21.031085
ENSDART00000158062.1 ENSDART00000158062  408.11734  451.99495   74.14371   66.968916
ENSDART00000172394.1 ENSDART00000172394  626.78916  471.64739  213.52186  264.217355
ENSDART00000170637.1 ENSDART00000170637  290.06519  427.62319  492.98162  502.917689
ENSDART00000176601.1 ENSDART00000176601  147.67898  130.11751  142.12726  129.322780
ENSDART00000127085.2 ENSDART00000127085  130.32099  141.88252   66.87272   80.677221
ENSDART00000169268.1 ENSDART00000169268  155.24162  129.12446  103.22608   59.437924
ENSDART00000167000.1 ENSDART00000167000  256.67582  284.13010  327.04572  367.689609
ENSDART00000166248.1 ENSDART00000166248  728.42970  652.77464  626.33181  629.949785
ENSDART00000163725.1 ENSDART00000163725  145.35091  162.39590  205.89374  237.519453
ENSDART00000108528.3 ENSDART00000108528  302.88237  249.19433    0.00000    0.000000
ENSDART00000042086.5 ENSDART00000042086 1570.76676 1454.40982 1709.10632 1775.480527

expression table:
                             isoform_id   inj_rep1   inj_rep2   uni_rep1   uni_rep2
ENSDART00000097631.4 ENSDART00000097631  0.8402959  0.8180524  1.6638950  2.0734843
ENSDART00000169443.1 ENSDART00000169443  2.4496215  2.7303391  3.3127219  3.1282718
ENSDART00000170158.1 ENSDART00000170158 13.8070987 12.9787441  0.0000000  0.3109213
ENSDART00000171794.2 ENSDART00000171794  4.1447246  4.9561189  3.9545024  4.5661950
ENSDART00000164713.1 ENSDART00000164713  3.6164655  3.2454172 21.9996404 28.8335483
ENSDART00000168732.1 ENSDART00000168732  7.7022575  6.7467509 46.7651711 52.4435354
ENSDART00000167905.1 ENSDART00000167905  7.7022575  6.7467509 24.7986770 37.0422804
ENSDART00000170411.1 ENSDART00000170411  1.0410377  1.0572490  1.0436173  1.2508349
ENSDART00000169846.1 ENSDART00000169846  2.7255590  2.2521894  0.7784337  0.7054784
ENSDART00000169539.1 ENSDART00000169539  1.3796176  1.7040895  0.9025473  1.1084834
ENSDART00000168709.1 ENSDART00000168709  1.4195597  1.6694551  0.4229552  0.4686325
ENSDART00000167456.1 ENSDART00000167456  1.7901539  0.8609540  1.4437951  0.8268825
ENSDART00000158062.1 ENSDART00000158062 10.0899049 10.4101805  2.3624478  2.6065204
ENSDART00000172394.1 ENSDART00000172394  5.7010487  3.9964405  2.5030037  3.7833842
ENSDART00000170637.1 ENSDART00000170637  2.6383286  3.6234074  5.7789626  7.2013848
ENSDART00000176601.1 ENSDART00000176601  2.1112942  1.7329597  2.6187457  2.9106563
ENSDART00000127085.2 ENSDART00000127085  1.6775814  1.7014562  1.1094408  1.6349558
ENSDART00000169268.1 ENSDART00000169268  8.4098364  6.5164423  7.2070031  5.0690765
ENSDART00000167000.1 ENSDART00000167000  2.8536987  2.9428156  4.6861644  6.4356194
ENSDART00000166248.1 ENSDART00000166248  7.6195214  6.3610084  8.4436534 10.3736553
ENSDART00000163725.1 ENSDART00000163725  0.9165777  0.9540019  1.6733260  2.3579606
ENSDART00000108528.3 ENSDART00000108528  2.0157871  1.5450106  0.0000000  0.0000000
ENSDART00000042086.5 ENSDART00000042086 11.2282419  9.6852203 15.7454480 19.9802908
localAnnotation were downloaded from ftp://ftp.ensembl.org/pub/release-91/gtf/danio_rerio/ and then subset by the isoform_id

Sessioninfo:

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] BSgenome.Drerio.UCSC.danRer10_1.4.2 BSgenome_1.48.0                     Biostrings_2.48.0                   XVector_0.20.0                      IsoformSwitchAnalyzeR_1.2.0        
 [6] cummeRbund_2.22.0                   Gviz_1.24.0                         rtracklayer_1.40.6                  GenomicRanges_1.32.7                GenomeInfoDb_1.16.0                
[11] IRanges_2.14.12                     S4Vectors_0.18.3                    fastcluster_1.1.25                  reshape2_1.4.3                      ggplot2_3.0.0                      
[16] RSQLite_2.1.1                       BiocGenerics_0.26.0                

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.12.0         bitops_1.0-6                matrixStats_0.54.0          bit64_0.9-7                 RColorBrewer_1.1-2          progress_1.2.0             
 [7] httr_1.3.1                  tools_3.5.1                 backports_1.1.2             R6_2.2.2                    rpart_4.1-13                Hmisc_4.1-1                
[13] DBI_1.0.0                   lazyeval_0.2.1              colorspace_1.3-2            nnet_7.3-12                 withr_2.1.2                 tidyselect_0.2.4           
[19] gridExtra_2.3               prettyunits_1.0.2           VennDiagram_1.6.20          curl_3.2                    bit_1.1-14                  compiler_3.5.1             
[25] Biobase_2.40.0              formatR_1.5                 htmlTable_1.12              DelayedArray_0.6.6          scales_1.0.0                checkmate_1.8.5            
[31] readr_1.1.1                 stringr_1.3.1               digest_0.6.17               Rsamtools_1.32.3            foreign_0.8-71              base64enc_0.1-3            
[37] dichromat_2.0-0             pkgconfig_2.0.2             htmltools_0.3.6             limma_3.36.5                ensembldb_2.4.1             htmlwidgets_1.3            
[43] rlang_0.2.2                 rstudioapi_0.7              bindr_0.1.1                 jsonlite_1.5                BiocParallel_1.14.2         acepack_1.4.1              
[49] dplyr_0.7.6                 VariantAnnotation_1.26.1    RCurl_1.95-4.11             magrittr_1.5                GenomeInfoDbData_1.1.0      Formula_1.2-3              
[55] futile.logger_1.4.3         Matrix_1.2-14               Rcpp_0.12.19                munsell_0.5.0               edgeR_3.22.4                stringi_1.2.4              
[61] MASS_7.3-50                 SummarizedExperiment_1.10.1 zlibbioc_1.26.0             plyr_1.8.4                  blob_1.1.1                  crayon_1.3.4               
[67] lattice_0.20-35             DRIMSeq_1.8.0               splines_3.5.1               GenomicFeatures_1.32.2      hms_0.4.2                   locfit_1.5-9.1             
[73] knitr_1.20                  pillar_1.3.0                biomaRt_2.36.1              futile.options_1.0.1        XML_3.98-1.16               glue_1.3.0                 
[79] biovizBase_1.28.2           latticeExtra_0.6-28         lambda.r_1.2.3              data.table_1.11.4           gtable_0.2.0                purrr_0.2.5                
[85] assertthat_0.2.0            AnnotationFilter_1.4.0      survival_2.42-6             tibble_1.4.2                GenomicAlignments_1.16.0    AnnotationDbi_1.42.1       
[91] memoise_1.1.0               tximport_1.8.0              bindrcpp_0.2.2              cluster_2.0.7-1            

ADD COMMENTlink written 12 days ago by Ou, Jianhong1.1k

Hello Ou, Jianhong!

We believe that this post does not fit the main topic of this site.

This is fixed in development version

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 12 days ago by Ou, Jianhong1.1k

Why does cryptic error messages not belong here?

ADD REPLYlink modified 11 days ago • written 11 days ago by k.vitting.seerup20
1

I just tried the development version. And I found that this issue is already resolved in the development version. So I closed the question by myself.

Thank you.

ADD REPLYlink modified 11 days ago • written 11 days ago by Ou, Jianhong1.1k

Take a look at this thread - the error seems similar - maybe the solution does as well.

ADD REPLYlink modified 11 days ago • written 11 days ago by k.vitting.seerup20
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 234 users visited in the last hour