epurdom
calling RSEC() function error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘primaryCluster’ for signature ‘"NULL"’
Hello,
I'm trying to run RSEC() on a data matrix that contains 1000 genes and 12170 cells. I got the error as below: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘primaryCluster’ for signature ‘"NULL"’
I also found a previous post on github related to this issue: https://github.com/epurdom/clusterExperiment/issues/182
However, the issue was with the clusterMany() function. I wonder if the issue with the RSEC() function has also something to do with the memory? I tried adding the argument "largeDataset=TRUE" in the RSEC() function but it didn't solve the problem. Can anyone help? Thanks very much!
The full code is:
RSEC(seObj, k0s = 3: 15, alphas = c(0.1), betas = 0.8, reduceMethod = "none", clusterFunction = "hierarchical01", minSizes = 1, ncores = NCORES, isCount = FALSE, dendroReduce = "none", dendroNDims=NA, subsampleArgs = list(resamp.num = 100, clusterFunction = "kmeans", clusterArgs = list(nstart = 10)), verbose = TRUE, consensusProportion = 0.7, mergeMethod = "none", random.seed = 424242, consensusMinSize = 10)
The traceback of the error is:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘primaryCluster’ for signature ‘"NULL"’
It could be related to memory -- the traceback is not very informative. What machine are you running it on -- in particular what is the memory capacity of the machine (and what is NCORES)?
The original dataset is not very large, but during subsampling, a 12K x 12K matrix is created to store the results, so that's roughly 1.5Gb for each instance. So if you are parallelizing across cores that could add up.
I'm running it on a cluster. I requested 16 cores, and each has 10.67GB memory capacity.
I got the same error and its due to processes being killed by the out-of-mamory handler.
