> plotDispEsts(dds)
Error in plot(rowMeans(counts(cds, normalized = TRUE)), fitInfo(cds)$perGeneDispEsts, : error in evaluating the argument 'y' in selecting a method for function 'plot': Error: could not find function "fitInfo"
Thanks for the help.
It looks like a collision between DESeq (old version) and DESeq2. This shouldn't happen if you use a recent version of Bioconductor.
Can you post sessionInfo()?
Your local version of Bioconductor software is:
source("http://bioconductor.org/biocLite.R")
biocVersion()
The current version of Bioconductor is 3.2. You can also find the current version here:
Thank you Michael. I do not have old DESeq attached as you can see below.
-----------------------------------------------------------------------------------------------------------------------------------------------------
> sessionInfo() R version 3.1.3 (2015-03-09) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final) locale: [1] C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq2_1.6.3 pheatmap_1.0.8 vsn_3.34.0 Biobase_2.26.0 [5] RColorBrewer_1.1-2 RcppArmadillo_0.6.500.4.0 Rcpp_0.12.3 GenomicRanges_1.18.4 [9] GenomeInfoDb_1.2.5 IRanges_2.0.1 S4Vectors_0.4.0 BiocGenerics_0.12.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.28.2 BBmisc_1.9 BatchJobs_1.6 BiocInstaller_1.16.5 BiocParallel_1.0.3 [6] DBI_0.3.1 Formula_1.2-1 Hmisc_3.17-1 KernSmooth_2.23-15 RSQLite_1.0.0 [11] XML_3.98-1.3 XVector_0.6.0 acepack_1.3-3.3 affy_1.44.0 affyio_1.34.0 [16] annotate_1.44.0 base64enc_0.1-3 bitops_1.0-6 brew_1.0-6 caTools_1.17.1 [21] checkmate_1.7.1 cluster_2.0.3 codetools_0.2-14 colorspace_1.2-6 digest_0.6.9 [26] fail_1.3 foreach_1.4.3 foreign_0.8-66 gdata_2.17.0 genefilter_1.48.1 [31] geneplotter_1.44.0 ggplot2_2.0.0 grid_3.1.3 gridExtra_2.0.0 gtable_0.1.2 [36] gtools_3.5.0 iterators_1.0.8 lattice_0.20-33 latticeExtra_0.6-26 limma_3.22.7 [41] locfit_1.5-9.1 magrittr_1.5 munsell_0.4.2 nnet_7.3-12 plyr_1.8.3 [46] preprocessCore_1.28.0 rpart_4.1-10 scales_0.3.0 sendmailR_1.2-1 splines_3.1.3 [51] stringi_1.0-1 stringr_1.0.0 survival_2.38-3 tools_3.1.3 xtable_1.8-2 [56] zlibbioc_1.12.0
----------------------------------------------------------------------------------
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help
A new version of Bioconductor is available after installing the most recent version of R; see
http://bioconductor.org/install
> biocVersion()
[1] ‘3.0’
----------------------------------------------
I also tried it with latest version of R and bioconductor.
-------------------------------------------------------------------------------------------------
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)
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] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1 vsn_3.38.0 gplots_2.17.0
[4] RColorBrewer_1.1-2 DESeq2_1.10.1 RcppArmadillo_0.6.500.4.0
[7] Rcpp_0.12.3 SummarizedExperiment_1.0.2 Biobase_2.30.0
[10] GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.6
[13] S4Vectors_0.8.11 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] futile.logger_1.4.1 plyr_1.8.3 XVector_0.10.0 bitops_1.0-6
[5] futile.options_1.0.0 tools_3.2.3 zlibbioc_1.16.0 rpart_4.1-10
[9] preprocessCore_1.32.0 annotate_1.48.0 RSQLite_1.0.0 gtable_0.1.2
[13] lattice_0.20-33 DBI_0.3.1 gridExtra_2.0.0 DESeq_1.22.1
[17] cluster_2.0.3 genefilter_1.52.1 caTools_1.17.1 gtools_3.5.0
[21] locfit_1.5-9.1 nnet_7.3-11 grid_3.2.3 AnnotationDbi_1.32.3
[25] XML_3.98-1.3 survival_2.38-3 BiocParallel_1.4.3 foreign_0.8-66
[29] limma_3.26.7 gdata_2.17.0 latticeExtra_0.6-26 Formula_1.2-1
[33] geneplotter_1.48.0 ggplot2_2.0.0 lambda.r_1.1.7 Hmisc_3.17-1
[37] scales_0.3.0 splines_3.2.3 xtable_1.8-2 colorspace_1.2-6
[41] KernSmooth_2.23-15 affy_1.48.0 acepack_1.3-3.3 munsell_0.4.2
[45] affyio_1.40.0
---------------------------------------------------------------------------------------------------------------
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocVersion()
[1] ‘3.2’
I appreciate your help.
J.
Hi Michael,
> plotDispEsts
standardGeneric for "plotDispEsts" defined from package "BiocGenerics"
function (object, ...)
standardGeneric("plotDispEsts")
<environment: 0x4c0e200>
Methods may be defined for arguments: object
Use showMethods("plotDispEsts") for currently available ones.
Thanks.
hi John,
I'm not sure I can figure this out without being able to explore on your computer.
I can tell you that the line of code contained in the error is referencing DESeq code, but actually that line doesn't exist in DESeq either. It's slightly different in DESeq:
https://github.com/Bioconductor-mirror/DESeq/blob/master/R/plotDispEsts.R#L26-L34
I did find code matching your error in some DESeq wrapper packages, however e.g.:
https://github.com/cran/rnaseqWrapper/blob/9228db45812cff6e3c902eab10161536268ccaf7/R/plotDispEsts.R
So, if these were loaded at the same time you could produce the error, that would explain it.
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version 2.3.6
Can you type "plotDispEsts" in the R terminal and see what comes back? You should get the function code and location. It looks like this function is overwritten from somewhere, and the code is a copy of the DESeq code.