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Question: Error: could not find function "findMarkers"
1
gravatar for ravi_patel_4
3 months ago by
ravi_patel_410
ravi_patel_410 wrote:

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"
ADD COMMENTlink modified 3 months ago • written 3 months ago by ravi_patel_410
1
gravatar for Aaron Lun
3 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

Make sure you're using the latest version of scran. We are currently at version 1.4.5 in release.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Aaron Lun17k

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by ravi_patel_410
1

You are probably running on an old version of R; for biocLite to 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/.

ADD REPLYlink written 3 months ago by Aaron Lun17k

Updating R and Bioconductor solved the problem. I can access the findMarkers function now. Thanks Aaron.

ADD REPLYlink written 3 months ago by ravi_patel_410

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             

ADD REPLYlink written 8 weeks ago by Ays0

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         

ADD REPLYlink written 8 weeks ago by Ays0

Pretty much what it says. You're calling findMarkers without an argument, and there's no matching method for a call to the generic with a missing argument. You need to supply a matrix or SCESet object as input to the function (or SingleCellExperiment in the next release).

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Aaron Lun17k
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