Entering edit mode
ravi_patel_4
▴
10
@ravi_patel_4-13820
Last seen 6.7 years ago
Hello,
I am trying to use a function "findMarkers" from "scran" package. The installation and loading of scran works fine as can be seen in the messages printed when "library (scran)" command is run (below). However, when I run the "findMarkers()" command, R throws an error that it can't find the function. This strange since the "scran" manuals describes this function but R cannot find it, or am I missing something? Any help is appreciated.
Thank you for your time.
----------------------------------------------------------
> library(scran)
Loading required package: BiocParallel
Loading required package: scater
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: ggplot2
Want to understand how all the pieces fit together? Buy the ggplot2
book: http://ggplot2.org/book/
Attaching package: 'scater'
The following object is masked from 'package:stats':
filter
> findMarkers()
Error: could not find function "findMarkers"
Hi Aaron.
Thanks for the reply. Apparently the biocLite installs scran-v1.2.2 by default. Is there anyway to get v1.4.5?
Thanks.
Best,
Ravi
EDIT------------
I found the scran-v1.4.5. However it seems to require R3.4 and my current R version is 3.3.2. Is there any way to install the scran-v1.4.5 with 3.3.2?
Thank you.
You are probably running on an old version of R; for
biocLiteto download the latest version of scran, you need R 3.4.0 or higher. If you do have the latest version of R and are still getting the wrong version of scran, try following the instructions in the "Troubleshoot BiocInstaller" section of https://www.bioconductor.org/install/.Updating R and Bioconductor solved the problem. I can access the findMarkers function now. Thanks Aaron.
Hi Aaron,
I am running into similar problem, although everything is up to date:
> findMarkers()
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘findMarkers’ for signature ‘"missing"’
Any suggestions?
Here is my sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /opt/sw/packages/intel/17.0.4/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] scran_1.4.5 BiocParallel_1.10.1 scater_1.4.0
[4] ggplot2_2.2.1 Biobase_2.36.2 BiocGenerics_0.22.0
[7] BiocInstaller_1.26.1
loaded via a namespace (and not attached):
[1] viridis_0.4.0 dynamicTreeCut_1.63-1 edgeR_3.18.1
[4] bit64_0.9-7 viridisLite_0.2.0 splines_3.4.1
[7] shiny_1.0.3 assertthat_0.2.0 statmod_1.4.30
[10] stats4_3.4.1 blob_1.1.0 vipor_0.4.5
[13] RSQLite_2.0 lattice_0.20-35 glue_1.1.1
[16] limma_3.32.7 digest_0.6.12 colorspace_1.3-2
[19] htmltools_0.3.6 httpuv_1.3.5 Matrix_1.2-10
[22] plyr_1.8.4 XML_3.98-1.9 pkgconfig_2.0.1
[25] biomaRt_2.32.1 zlibbioc_1.22.0 xtable_1.8-2
Hi Aaron,
I am running into similar problem, although everything is up to date:
> findMarkers()
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘findMarkers’ for signature ‘"missing"’
Any suggestions?
Here is my sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /opt/sw/packages/intel/17.0.4/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] scran_1.4.5 BiocParallel_1.10.1 scater_1.4.0
[4] ggplot2_2.2.1 Biobase_2.36.2 BiocGenerics_0.22.0
[7] BiocInstaller_1.26.1
loaded via a namespace (and not attached):
[1] viridis_0.4.0 dynamicTreeCut_1.63-1 edgeR_3.18.1
[4] bit64_0.9-7 viridisLite_0.2.0 splines_3.4.1
[7] shiny_1.0.3 assertthat_0.2.0 statmod_1.4.30
[10] stats4_3.4.1 blob_1.1.0 vipor_0.4.5
[13] RSQLite_2.0 lattice_0.20-35 glue_1.1.1
[16] limma_3.32.7 digest_0.6.12 colorspace_1.3-2
[19] htmltools_0.3.6 httpuv_1.3.5 Matrix_1.2-10
[22] plyr_1.8.4 XML_3.98-1.9 pkgconfig_2.0.1
[25] biomaRt_2.32.1 zlibbioc_1.22.0 xtable_1.8-2
Pretty much what it says. You're calling
findMarkerswithout an argument, and there's no matching method for a call to the generic with a missing argument. You need to supply a matrix orSCESetobject as input to the function (orSingleCellExperimentin the next release).