Hi all,

I am trying to use maSigPro to conduct time-course analyis with only one condition. However, it is not feasible. I have checked the guideline or other blogs, but there is no answer. I wonder how to realize this. Thank you!

I use the example data here for practice.

library(maSigPro)
data(data.abiotic) 
data(edesign.abiotic)
edesign.abiotic <- as.data.frame(edesign.abiotic)
design.n <- edesign.abiotic[1:9,1:3]
data.n <- data.abiotic[,rownames(design.n)]

colnames(design.n) <-c("Time","Replicate","Group")
design <- make.design.matrix(design.n)
design$groups.vector
# [1] "Group" "Group"
head(design.n)

#             Time  Replicate   Group
#Control_3H_1   3   1   1   
#Control_3H_2   3   1   1   
#Control_3H_3   3   1   1   
#Control_9H_1   9   2   1   
#Control_9H_2   9   2   1   
#Control_9H_3   9   2   1   

head(data.n)
#        Control_3H_1  Control_3H_2  Control_3H_3  Control_9H_1  Control_9H_2
#STMDF90    0.13735714  -0.36530651 -0.15329448 0.44754535  0.287476796 
#STMCJ24    NA  NA  NA  NA  NA  
#STMJH42    0.07864449  0.10023285  -0.17365488 -0.25279484 0.184855409 
#STMDE66    0.22976991  0.47409748  0.46930716  0.37101059  -0.004992029    
#STMIX74    0.14407618  -0.48018637 -0.07847999 0.05692331  0.013045420 
#STMCL34    0.06494078  0.04472986  0.04280790  0.16128091  0.088048892 

fit <- p.vector(data.n,
                design,
                Q = 0.05,
                MT.adjust = "BH", 
                min.obs = 20)

# Error in dat[i, ] : subscript out of bounds

You have a data.frame with 9 columns and are specifying a minimum of 20 observations per gene. Since you don't have 20 observations for any gene, it fails.

> fit <- p.vector(data.n,
                design,
                Q = 0.05,
                MT.adjust = "BH", min.obs = 9)
[1] "fitting  gene 100 out of 725"
[1] "fitting  gene 200 out of 725"
[1] "fitting  gene 300 out of 725"
[1] "fitting  gene 400 out of 725"
[1] "fitting  gene 500 out of 725"
[1] "fitting  gene 600 out of 725"
[1] "fitting  gene 700 out of 725"
[1] "no significant genes"
>