Entering edit mode
3.6 years ago
pthom010
▴
40
I have a csv file with the log2 scores of eight different timepoints. The header of the table looks like this:
head(templogs)
SB SC SD SE
TRINITY_DN1001_c0_g1_i1 -0.5638283 -1.2861425 -0.8790812 -1.9667007
TRINITY_DN1001_c0_g1_i5 -0.3484778 -0.8097831 -0.3951722 -1.2755624
TRINITY_DN1001_c0_g2_i1 -0.4141790 -1.4300189 -1.0538773 -2.3604466
TRINITY_DN1001_c2_g1_i1 -0.3890476 -1.5069918 -0.9539496 -2.4254780
TRINITY_DN10027_c0_g1_i2 -0.2425431 0.4412087 0.4699400 0.7566083
TRINITY_DN10030_c0_g1_i1 1.0605554 0.4989614 0.2710047 0.8756346
RB RC RD RE
TRINITY_DN1001_c0_g1_i1 -0.29717574 -0.8332547 -0.8467823 -1.343256
TRINITY_DN1001_c0_g1_i5 -0.45046536 -0.9659265 -1.1268979 -1.572577
TRINITY_DN1001_c0_g2_i1 -0.49264872 -1.0463790 -1.1199727 -1.916905
TRINITY_DN1001_c2_g1_i1 -0.58782459 -1.0346161 -1.0258695 -1.920455
TRINITY_DN10027_c0_g1_i2 -0.03957106 0.7577178 0.6700604 1.681934
TRINITY_DN10030_c0_g1_i1 4.94468049 5.6052340 6.0095423 4.954922
The table has about 2100 rows. What I would like to do is k-means clustering on the matrix and use those results to cluster my rows on a heatmap. However, I seem to be having issues with the hclust function in R. Here is how far I have gotten:
km = kmeans(templogs, centers = 2)$cluster
I then try to run
rows = hclust(templogs)$order
but get the following error message:
Error in if is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") :
missing value where TRUE/FALSE needed
Would anybody by chance know how to resolve this issue. I am also trying to use the split function with the km$cluster object I made before but I am getting this error message:
Error in Heatmap(templogs, row_order = d, split = cluster) :
object 'cluster' not found
I'm not sure how to resolve this. Alternatively, if anybody has any suggestions to make this easier, I am also receptive to those.Thanks.
