Entering edit mode
Dear,
We have a Single Series Time Course and we would like to analyse it on
maSigPro.
But we got an error in see.genes:
> see.genes(sigs, design, main = "Exp Prof MI", show.fit = T,
+ dis = design$dis, cluster.method="kmeans", cluster.data = 1, k = 9)
Error in edesign[, time.col] : incorrect number of dimensions
sig.genes function is OK.
> sigs <- get.siggenes(tstep, rsq = 0.6, vars = "each")
> sigs$summary
if (stringsAsFactors) factor(x) else x
1 AD1X1FD8 (1)
2 AD1X1FD8 (2)
(...)
136 ST3X9BD3 (1)
137 ST3X7DD0 (2)
my design file (degree = 4):
> design
$dis
Time Time2 Time3 Time4
Array1 1 1 1 1
Array2 1 1 1 1
Array3 1 1 1 1
Array4 5 25 125 625
Array5 5 25 125 625
Array6 5 25 125 625
Array7 9 81 729 6561
Array8 9 81 729 6561
Array9 9 81 729 6561
Array10 13 169 2197 28561
Array11 13 169 2197 28561
Array12 13 169 2197 28561
Array13 17 289 4913 83521
Array14 17 289 4913 83521
Array15 17 289 4913 83521
$groups.vector
[1] "Group" "Group" "Group" "Group"
$edesign
Time Replicates Group
Array1 1 1 1
Array2 1 1 1
Array3 1 1 1
Array4 5 2 1
Array5 5 2 1
Array6 5 2 1
Array7 9 3 1
Array8 9 3 1
Array9 9 3 1
Array10 13 4 1
Array11 13 4 1
Array12 13 4 1
Array13 17 5 1
Array14 17 5 1
Array15 17 5 1
>
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-pc-mingw32
locale:
LC_COLLATE=Portuguese_Brazil.1252;LC_CTYPE=Portuguese_Brazil.1252;LC_M
ONETARY=Portuguese_Brazil.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Brazil.
1252
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods base
other attached packages:
[1] maSigPro_1.10.0 Biobase_1.16.3
>
Could you help me? What I could do wrong?
Thank you very much.
--
Marcelo Luiz de Laia
Jaboticabal - SP - Brazil
"Voc? v? as coisas como elas s?o e pergunta: por qu?? Mas eu sonho com
coisas que nunca foram e pergunto: por que n?o? " - Bernard Shaw
