Displaying 2 results from an estimated 2 matches for "progenetixcrc".
2006 Jul 10
2
pvclust missing values problem
...below.
band sample1 sample2 sample3 sample4
1p36_33 1 0 0 1
1p36_32 -1 0 -1 0
1p36_31 0 1 1 1
1p36_22 0 -1 -1 -1
etc.... where 0 = no change, 1 = gain, -1 = loss
I have read this file into R using:
> ProgenetixCRC.all.noXY <- read.table("/home/marraydb/Progenetix/Data/CRCall_noXY.txt", header=TRUE, sep="\t", row.names="band")
based on the pvclust documentation I came up with this:
>ProgenetixCRC.all.pvclust <- pvclust(ProgenetixCRC.all, method.dist="cor", met...
2006 Jul 06
0
pvclust Error:NA/NaN/Inf in foreign function call (arg 11)
...as a table where each column is a single case and each row is a single chromosome band. The value in each cell is either 0, 1, 2, or -1. Corresponding to no change, gain, high level amplification, or loss respectively Based on the documentation for the pvclust package I came up with this code.
>ProgenetixCRC.all.pvclust <- pvclust(ProgenetixCRC.all, method.dist="cor", method.hclust="average",use.cor="pairwise.complete.obs",nboot=1000)
this results in the following error
Bootstrap (r = 0.5)... Error in hclust(distance, method = method.hclust) :
NA/NaN/Inf in foreign...