Question: champ.norm task 1 failed - "could not find function "blc""
0
gravatar for zkun8638
8 weeks ago by
zkun863810
zkun863810 wrote:

When using champ.norm to process the data, the following error occurred. And it dosen‘t work and shows the same error after I load the RPMM package:

> library(RPMM)

Loading required package: cluster

> myNorm <- champ.norm(beta=myLoad$beta,arraytype="450K",cores=5)
[===========================]
[>>>>> ChAMP.NORM START <<<<<<]
-----------------------------
champ.norm Results will be saved in ./CHAMP_Normalization/

[ SWAN method call for BOTH rgSet and mset input, FunctionalNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

<< Normalizing data with BMIQ Method >>

Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).

5 cores will be used to do parallel BMIQ computing.

Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(beta)[x],  :

  task 1 failed - "could not find function "blc""
forum software error • 175 views
ADD COMMENTlink modified 8 weeks ago by Carlo Yague5.7k • written 8 weeks ago by zkun863810

Hello kun8638,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

ADD REPLYlink written 8 weeks ago by Carlo Yague5.7k

Hello kun8638!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/p133866/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Carlo Yague5.7k

sorry,I already deleted the other post

ADD REPLYlink written 8 weeks ago by zkun863810

Thank you. In the future, if you feel that there is some value in cross-posting (some of us are not in both forums after all), you can do it, but make sure to add a disclaimer in your post with a direct link to the other site. That way we do not duplicate efforts to provide answers.

ADD REPLYlink written 8 weeks ago by Carlo Yague5.7k
2
gravatar for Carlo Yague
8 weeks ago by
Carlo Yague5.7k
Canada
Carlo Yague5.7k wrote:

Have you tried re-installing the RPMM and ChAMP packages ?

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChAMP")
install.packages("RPMM", dependencies=T)
ADD COMMENTlink modified 8 weeks ago • written 8 weeks ago by Carlo Yague5.7k

I am operating on a rented server, therefore I don't have the authoritation to install packages. Can you tell me what are the dependencies of RPMM packages?

ADD REPLYlink written 8 weeks ago by zkun863810

Can you tell me what are the dependencies of RPMM packages?

ENmix, MEAT, MethylMix

I don't have the authoritation to install packages.

Can you contact an administrator to help you with the issue ? Because if you can't install anything, not even a R package, then there is not much you can do about your issue.

ADD REPLYlink written 8 weeks ago by Carlo Yague5.7k
1

I have contacted the administrator,Thank you for the suggestions. The problem was fixed after re-installation of the RPMM and ChAMP packages

ADD REPLYlink written 8 weeks ago by zkun863810
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