multiple errors in flowSOM- with readinput and metaClustering_consensus
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@jeremyeadler-11401
Last seen 6.3 years ago

Hi all,

I've just started using flowsom and ive run into a few issues:

1. flowsom takes direct input of the fcs files but wont take a flowset directly

 fs<-read.flowSet(jfiles.out)
> fs
A flowSet with 8 experiments.

fs=ReadInput(fset)
Error in ReadInput(fset) : Inputs of type list are not supported. 
                    Please supply either a FlowFrame, a FlowSet or an array
                    of valid paths to files or directories.

However I've been able to use readinput directly:

> fs=ReadInput(jfiles.out)
Reading file TCGA-05-4244-01Z-00-DX1_19500_19500_500_500_LUAD/TCGA-05-4244-01Z-00-DX1_19500_19500_500_500_LUAD_jun_human.fcs ....

2. I get an error message when using metaclustering_consensus

the following work:

fs2=BuildSOM(fs)

fs3<-BuildMST(fs2)

then i try:

fs4=metaClustering_consensus(fs3,k=10)
Error in ConsensusClusterPlus::ConsensusClusterPlus(t(data), maxK = k,  : 
  d must be a matrix, distance object or ExpressionSet (eset object)

 

Thanks for your help!

jeremy

flowcore flowsom • 799 views
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@jeremyeadler-11401
Last seen 6.3 years ago

problem with clustering solved :  fs4=metaClustering_consensus(fs3:map:codes,k=10

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