Error using "timecourse" package for microaaray data.
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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?

microarray bioconductor RNA-Seq R • 1.7k views