Hi,

I have 6 RNA-Seq samples in different time points and I would like to find DE genes changes during developmental stages. My samples are:

I am trying to understand and use “maSigPro” to find DE genes during different developmental stages.

Here is what I did:

normData <- read.delim(normCounts, row.names=1, header=TRUE);

colData= read.delim(samples, row.names=1, header=TRUE)

keep <- rowSums(cpm(normData)>1) >= 2

countdz <- normData [ keep, ]

My question is: considering above table, could you please help me to make my edesign table? I have already tried the below but I got error message when calling p.vector()…

colnames(countdz)

rownames(colData)

edesign <- as.data.frame(cbind(colData$Time, colData$Replicate))

design <- make.design.matrix(edesign, degree=2)

What does the following mean? Why there is NA in timepoint comparison?

> design$groups.vector

[1] NA   "V2" NA   "V2"

> fit <- p.vector(countdz, design, Q = 0.05, MT.adjust = "BH", counts = TRUE)

Error in dat[, as.character(rownames(dis))] : subscript out of bounds

> tstep <- T.fit(fit, alfa = 0.05)

[1] "fitting gene 100 out of 363"

[1] "fitting gene 200 out of 363"

[1] "fitting gene 300 out of 363"

Error in if (group != indepen) { : missing value where TRUE/FALSE needed

Could you please help me to correct my “edesign” and also subsequent error messages?

Thanks

Simon