PAM analysis
Hello , I have implemented PAM , on a gene list from Rnaseq data to find the expression pattern of genes using the following code. The matrix holds the log fold change values of the contrast.
scale(c3)
pam.res <- pam(c3,4 )
pam.res$clusinfo
head(pam.res$clustering)
x11()
fviz_cluster(pam.res)
x11()
plot(silhouette(clara.res),main='Clara4CLUSTERS')
Can a gene downregulated in one sample and upregulated in another sample be in one cluster?? and why ?
and also how can I optimize the PAM functions to improve my results?
Any help would be highly appreciated
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