msSigPro packages error in edesign

unique379 · 11-05-2014, 02:39 AM

Dear all,

I am trying to use maSigPro packages for my next generation counts data. If someone have expression pls help me.
I have one experimental condition with replicates and their corresponding times (4 time point).
my script is as follows:
wt <- read.table("glmNB_wt_r.txt", header=T)
wt.edesign <- read.table("edesign_wt_r.txt", header=T)
d <- make.design.matrix (wt.edesign, degree=4) ### i guess i have 4 times thats why degree should be 4
head (d)

> head (d)
$dis
Time Time2 Time3 Time4
WT.T1.1 1 1 1 1
WT.T1.2 1 1 1 1
WT.T1.3 1 1 1 1
WT.T2.1 12 144 1728 20736
...........
............
WT.T4.6 36 1296 46656 1679616

$groups.vector
[1] "Group" "Group" "Group" "Group"

$edesign
Time Replicates Group
WT.T1.1 1 1 1
WT.T1.2 1 1 1
WT.T1.3 1 1 1
WT.T2.1 12 2 1
WT.T2.2 12 2 1
WT.T2.3 12 2 1
WT.T2.4 12 2 1
WT.T3.1 21 3 1
WT.T3.2 21 3 1
WT.T3.3 21 3 1
WT.T3.4 21 3 1
WT.T4.1 36 4 1
WT.T4.2 36 4 1
WT.T4.3 36 4 1
WT.T4.4 36 4 1
WT.T4.5 36 4 1
WT.T4.6 36 4 1

library(MASS)
> NBp <- p.vector (wt, d, counts =T)
[1] "fitting gene 100 out of 1194"
[1] "fitting gene 200 out of 1194"
.......
[1] "fitting gene 1100 out of 1194"
> NBt <- T.fit(NBp)
[1] "fitting gene 100 out of 384"
[1] "fitting gene 200 out of 384"
[1] "fitting gene 300 out of 384" ### end

> get <- get.siggenes(NBt, vars= "each")
> get$summary
independ Time Time2 Time3
1 mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p
......
....

Time4
1 mmu-miR-206-3p
2 mmu-miR-490-3p
3 ....... ###blank lines

> see.genes(get$sig.genes)
Error in 3:ncol(edesign) : argument of length 0 ?????

What is the problem here ?? help me please.

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11-05-2014, 02:39 AM	#1
unique379 Member Location: Italy Join Date: Aug 2012 Posts: 27	msSigPro packages error in edesign Dear all, I am trying to use maSigPro packages for my next generation counts data. If someone have expression pls help me. I have one experimental condition with replicates and their corresponding times (4 time point). my script is as follows: wt <- read.table("glmNB_wt_r.txt", header=T) wt.edesign <- read.table("edesign_wt_r.txt", header=T) d <- make.design.matrix (wt.edesign, degree=4) ### i guess i have 4 times thats why degree should be 4 head (d) > head (d) $dis Time Time2 Time3 Time4 WT.T1.1 1 1 1 1 WT.T1.2 1 1 1 1 WT.T1.3 1 1 1 1 WT.T2.1 12 144 1728 20736 ........... ............ WT.T4.6 36 1296 46656 1679616 $groups.vector [1] "Group" "Group" "Group" "Group" $edesign Time Replicates Group WT.T1.1 1 1 1 WT.T1.2 1 1 1 WT.T1.3 1 1 1 WT.T2.1 12 2 1 WT.T2.2 12 2 1 WT.T2.3 12 2 1 WT.T2.4 12 2 1 WT.T3.1 21 3 1 WT.T3.2 21 3 1 WT.T3.3 21 3 1 WT.T3.4 21 3 1 WT.T4.1 36 4 1 WT.T4.2 36 4 1 WT.T4.3 36 4 1 WT.T4.4 36 4 1 WT.T4.5 36 4 1 WT.T4.6 36 4 1 library(MASS) > NBp <- p.vector (wt, d, counts =T) [1] "fitting gene 100 out of 1194" [1] "fitting gene 200 out of 1194" ....... [1] "fitting gene 1100 out of 1194" > NBt <- T.fit(NBp) [1] "fitting gene 100 out of 384" [1] "fitting gene 200 out of 384" [1] "fitting gene 300 out of 384" ### end > get <- get.siggenes(NBt, vars= "each") > get$summary independ Time Time2 Time3 1 mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p mmu-miR-106b-5p ...... .... Time4 1 mmu-miR-206-3p 2 mmu-miR-490-3p 3 ....... ###blank lines > see.genes(get$sig.genes) Error in 3:ncol(edesign) : argument of length 0 ????? What is the problem here ?? help me please.