Question: Error using "timecourse" package for microaaray data.
0
unique37990 wrote:

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, fowwling 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 plz ??? where i m doing wrong ??

rna-seq microarray bioconductor R • 1.3k views