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Wuschel ▴ 10@wuschel-15944
Last seen 26 days ago
I am using
DEP package for analysis of deferentially enriched proteins. I get an error when testing comparisions, this same scripts worked in my old PC.
data_diff_manual <- test_diff(data_imp_knn, type = "manual", + test = c('mut_0h__vs_WT_0h_', + 'mut_0h__vs_WT_0h_', + 'mut_0h__vs_WT_0h_'))
Error: se does not inherit from class SummarizedExperiment
How can I fix this?
Please provide more information, so that I have a working example of the error. The error states that one of your input objects that should be of the class SummarizedExperiment, which is the object class that the DEP package is working with, is not a SummarizedExperiment.
deleted entry: double entry
This is my R details;
This is Package details details:
For installation problems, be sure that you are in a new R session with no other R sessions running. Use the command
BiocManager::valid()to check that you have a consistent installation.
It looks like you're trying to use a 'devel' version of DEP (the odd number, '.7' in the version) and you're trying to install from source. Instead, either install the current release version
BiocManager::install("DEP")or upgrade your entire installation to 'devel'
BiocManager::install(version="devel")and then install the devel version of DEP
I do not have any experience with DEP, but installing inconsistent versions of packages is likely to result in the types of errors you are reporting.
Hi Martin, Thank you for helping with this. This is my session info after reinstalling everything. Unfortunately Still I get this
"Error: se does not inherit from class SummarizedExperiment "
From the documentation
?test_diffand Arne's answer, it seems like your object
data_imp_knnshould be a SummarizedExperiment, i.e.,
is(data_imp_knn, "SummarizedExperiment")should return TRUE. Does it?