Hi All,
I am new to ConsensusClusterPlus. I followed its tutorial in Bioconductor:
d = read.table("data.txt",header=T)
# Choose the top 5000 most variable genes
mads=apply(d,1,mad)
d=d[rev(order(mads))[1:5000],]
# Normalize the data
d = sweep(d,1, apply(d,1,median,na.rm=T))
# Do clustering
results = ConsensusClusterPlus(d,maxK=6,reps=50,pItem=0.8,pFeature=1,
clusterAlg="hc",distance="pearson",
writeTable = T, seed=seed,plot="pdf")
I got an error:
Error in ConsensusClusterPlus(d, maxK = maxK, reps = 50, pItem = 0.8, :
d must be a matrix, distance object or ExpressionSet (eset object)
I then checked
d[1:5,1:5]
X011453b6 X0120b5b1 X01234d47 X01d4c289 X02334a5d
KLK3 39297.272 -376296.10 -222358.676 -139770.162 41272.738
ACPP -63803.954 -84514.79 -78520.053 -52781.560 -14151.932
KLK2 -26682.169 -126980.85 -38054.406 -27969.737 -62030.083
MYH11 108555.886 104602.45 -13819.642 -3358.701 106187.125
EEF2 8784.966 -38319.96 -1088.419 2986.275 -9114.912
It looks like d is a matrix. Am I missing something so the error pops up?
Thanks!