maSigPro edesign and error message
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simonjean434 ▴ 10
@simonjean434-7535
Last seen 7.4 years ago
Canada

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:

Sample

Time

Replicate

Tissue

Sample1

day1

1

Liver

Sample2

day1

1

Liver

Sample3

day7

2

Liver

Sample4

day7

2

Liver

Sample5

day12

3

Liver

Sample6

day12

3

Liver

 

 

 

 

 

 

 

 

 

 

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

masigpro • 1.3k views
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Entering edit mode

Hello,

I am also facing same error in my analysis. Have you got reply for this?

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