Entering edit mode
Heike Pospisil
▴
310
@heike-pospisil-1097
Last seen 10.2 years ago
Hello Bioconducters,
I used t-test and/or SAM to find significant genes describing the
differences in
hgu133plus2-chips of two different phenotypical classes. The resulting
heatmaps
show a promising clustering.
Now, I would like to confirm these clusters and to estimate the
robustness of
this clustering by cross-validation and/or bootstrapping(*). For that,
I have
two questions:
1) Does there exists an appropriate package and/or source to perfom
cross-validation and/or bootstrapping?
2) Which is the right measure to rate the goodness of such a
clustering? By now,
I looked over the cluster plots(**) and decided if it was good or a
bad clustering.
Thanks in advance for any suggestion.
Best wishes,
Heike
* with varying chip - subsets
** heatmap(exprs(sub),Colv=as.dendrogram(hclust(dist(t(exprs(sub)),
method="euclidean"),method="complete")))