JunctionSeq Can't produce Summary Plots
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Entering edit mode
@rachelrodgers12-12901
Last seen 4.4 years ago

Hi,

I have run JunctionSeq on a large RNA-seq data set, and have managed to produce the comprehensive set of plots using buildAllPlots() following the JunctionSeq user manual.  However, when I try to run plotDispEsts(jscs), a plot is produced but seems corrupted and won't open.  Here is the output to the console which looks like things are running ok:

> plotDispEsts(jscs)
     abundance ranges from 0.010150733280822 to 288462.038735504
     dispersion ranges from 1.00626741453259e-06 to 104
     Plotting dispersions from 0.00112604526834281 to 104

Next when I try to plotMA(jscs, FDR.threshold=0.05) I receive this error:

Error in plotMA(jscs, FDR.threshold = 0.05) :
  Error: you must specify the name of the column containing the desired fold change variable.

I have tried consulting the manuals to see what argument I am missing, but I can't find it.

Any help is appreciated,

Rachel

sessionInfo()

Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)

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] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] Cairo_1.5-9                BiocInstaller_1.24.0
 [3] JunctionSeq_1.4.0          SummarizedExperiment_1.4.0
 [5] Biobase_2.34.0             GenomicRanges_1.26.3
 [7] GenomeInfoDb_1.10.3        IRanges_2.8.1
 [9] S4Vectors_0.12.1           BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0    statmod_1.4.29       locfit_1.5-9.1
 [4] splines_3.3.3        lattice_0.20-35      colorspace_1.3-2
 [7] htmltools_0.3.5      base64enc_0.1-3      survival_2.41-3
[10] XML_3.98-1.5         DBI_0.6              foreign_0.8-67
[13] BiocParallel_1.8.1   RColorBrewer_1.1-2   plyr_1.8.4
[16] stringr_1.2.0        zlibbioc_1.20.0      munsell_0.4.3
[19] gtable_0.2.0         DESeq2_1.14.1        htmlwidgets_0.8
[22] memoise_1.0.0        latticeExtra_0.6-28  knitr_1.15.1
[25] geneplotter_1.52.0   AnnotationDbi_1.36.2 htmlTable_1.9
[28] Rcpp_0.12.9          acepack_1.4.1        xtable_1.8-2
[31] scales_0.4.1         backports_1.0.5      checkmate_1.8.2
[34] plotrix_3.6-4        Hmisc_4.0-2          annotate_1.52.1
[37] XVector_0.14.0       gridExtra_2.2.1      ggplot2_2.2.1
[40] digest_0.6.12        stringi_1.1.2        grid_3.3.3
[43] tools_3.3.3          bitops_1.0-6         magrittr_1.5
[46] RSQLite_1.1-2        lazyeval_0.2.0       RCurl_1.95-4.8
[49] tibble_1.2           Formula_1.2-1        cluster_2.0.6
[52] Matrix_1.2-8         data.table_1.10.4    assertthat_0.1
[55] rpart_4.1-10         nnet_7.3-12

 

 

JunctionSeq • 444 views
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Entering edit mode

Update:  found dispersion and MA plots within the directory with all other plots produced by buildAllPlots().  I assume this is what I am looking for.

Rachel

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