Hello Bioconductor team,

Can you help me .  I try to see the dendogram of the clustering of my data. 
I use the HOPACH package first hopach fonction and in a second time hopach2tree which generate a .cdt and a gtr file.
the .cdt does not work with javatreeview

here my code:
 
> data = read.csv2("EXP1_3_HOPACH_11.2_18.5_Log2FC0.32_p0.01.csv", h = T)
> 
> 
> gene.dist = distancematrix(data, "cor", na.rm=TRUE)
Warning message:
In cor(t(X), use = na) : NAs introduits lors de la conversion automatique
> 
> 
> gene.hobj = hopach(data, dmat = gene.dist)
> 
> hopach2tree(data, file = "HOPACH_Tree",
+  hopach.genes = gene.hobj,
+  hopach.arrays = NULL, dist.genes = NULL, 
+  dist.arrays = NULL, d.genes = "cor", 
+  d.arrays = NULL,
+  gene.wts = NULL,
+  array.wts = NULL,
+  gene.names = data[,1])
GENE TREE:
Working on level 13 
Working on level 12 
Working on level 11 
Working on level 10 
Working on level 9 
Working on level 8 
Working on level 7 
Working on level 6 
Working on level 5 
Working on level 4 
Working on level 3 
Working on level 2 
Working on level 1 
ARRAY TREE:
Only one level in array tree: no .atr file created 
Warning message:
In cor(t(X), use = na) : NAs introduits lors de la conversion automatique
> 
> 


Thanks in advance for your reply

Sebastien
	[[alternative HTML version deleted]]

