Entering edit mode

8.9 years ago

unique379
▴
110

Dear all,

I am trying to analyze my time course microarray data. I have 4 time and two biological groups (A and B). Unfortunately, my all time pints **do not have equal replicates** (i.e **T1** (R1,R2,R3), **T2** (R1,R2,R3,R4), **T3** (R1,R2,R3,R4), and **T4** (R1,R2,R3,R4,R5,R6), respectively dim (16917 34)). Therefore, following user guide of timecourse, I inserted NA in corresponding missing time replicates in every missing time. so, my matrix become dim (16917 48). And matrix looks like

```
T1 (R1,R2,R3, R4,R5,R6), T2 (R1,R2,R3,R4,R5,R6), T3 (R1,R2,R3,R4,R5,R6), T4(R1,R2,R3,R4,R5,R6)
g1 12 13 4 NA NA NA 2 4 6 67 NA NA 3 5 6 7 NA NA 43 65 83 6 7 0
..
..
```

and done analysis with follwoing code:

```
size = matrix(6, nrow = 16917, ncol = 2)
## condition group
c.grp <- as.character(rep(c("A","B"),each=24))
## time group (must be numeric)
t.grp <- as.numeric(rep(c(1:4,1:4,1:4,1:4), 3))
## rep grp
r.grp=rep(rep(c("T1","T2","T3","T4"),each=6),2)
## Calculate the M B-statistics and T2 statistics and plot individual genes of interest
time.results = mb.long(A.B.matrix, times=4, method= "2D", reps=size, condition.grp=c.grp, time.grp=t.grp, rep.grp=r.grp,out.t = T, HotellingT2.only=F)
```

and GOT ERROR:

```
Error in mb.2D(object, times, reps, prior.df, prior.COV, prior.eta, condition.grp, :
16917 genes may have within replicate missing values.
```

Help me please! What am I doing wrong?