Hi Thoma Hi James Thanks a lot for your help. @ Thomas: u r right, that did it. @ James: I emailed the data, but thanks a lot its solved already :) Thanks a lot yours, Alyaa On Sat, Jun 2, 2012 at 6:14 PM, Thomas Girke <thomas.girke@ucr.edu> wrote: > You probably forgot to remove the zero variance columns in your matrix. In > the > step where you are observing the error you are clustering the columns of > bb not > its rows, since the cor() functions operates on the columns of a matrix > not its > rows. Running things stepwise might help to pinpoint the problem: > > ## Sample data > bb <- matrix(1:5, 5, 5, dimnames=list(paste("g", 1:5, sep=""), paste("t", > 1:5, sep="")), byrow=TRUE)> bb > t1 t2 t3 t4 t5 > g1 1 2 3 4 5 > g2 1 2 3 4 5 > g3 1 2 3 4 5 > g4 1 2 3 4 5 > g5 1 2 3 4 5 > > > bb > t1 t2 t3 t4 t5 > g1 1 2 3 4 5 > g2 1 2 3 4 5 > g3 1 2 3 4 5 > g4 1 2 3 4 5 > g5 1 2 3 4 5 > > ## cor() without t() > > cor(bb) > t1 t2 t3 t4 t5 > t1 1 NA NA NA NA > t2 NA 1 NA NA NA > t3 NA NA 1 NA NA > t4 NA NA NA 1 NA > t5 NA NA NA NA 1 > Warning message: > In cor(bb) : the standard deviation is zero > > ## cor() with t() > > cor(t(bb)) > g1 g2 g3 g4 g5 > g1 1 1 1 1 1 > g2 1 1 1 1 1 > g3 1 1 1 1 1 > g4 1 1 1 1 1 > g5 1 1 1 1 1 > > ## hclust without t() > > hc <- hclust(as.dist(1-cor(bb))) > Error in hclust(as.dist(1 - cor(bb))) : > NA/NaN/Inf in foreign function call (arg 11) > In addition: Warning message: > In cor(bb) : the standard deviation is zero > > ## hclust with t() > hc <- hclust(as.dist(1-cor(t(bb)))) > > Thomas > > On Sat, Jun 02, 2012 at 12:57:46PM +0000, Alyaa Mahmoud wrote: > > Hi All > > > > I am trying to cluster 57 COGs in 24 datasets. I use the following code > and > > run into this error: > > > > hc = NULL > > hc <- hclust(as.dist(1-cor(as.matrix(bb), method="spearman")), > > method="complete", members=NULL) > > > > Error in hclust(as.dist(1 - cor(as.matrix(bb), method = "spearman")), : > > NA/NaN/Inf in foreign function call (arg 11) > > In addition: Warning message: > > In cor(as.matrix(bb), method = "spearman") : the standard deviation is > zero > > > > hr = NULL > > hr <- hclust(as.dist(1-cor(t(as.matrix(bb)), method="spearman")), > > method="complete", members=NULL) > > > > I tried to remove any rows that have sd of zero but there was none; > > ind <- apply(bb, 1, var) == 0 > > subset <- bb[!ind,] > > > > or > > > > ind <- apply(bb, 1, sd) == 0 > > subset <- bb[!ind,] > > > > > > any clue what coule the problem be ? > > > > Thanks a lot for your help > > yours, > > Alyaa > > -- > > Alyaa Mahmoud > > > > "Love all, trust a few, do wrong to none"- Shakespeare > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]