HOPACH and .cdt which doesn't work with javatreeview
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@sebastien-tourlet-2613
Last seen 6.8 years ago
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]]
Clustering hopach Clustering hopach • 551 views
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