Question: maSigPro edesign and error message
0
gravatar for simonjean434
3.6 years ago by
simonjean43410
Canada
simonjean43410 wrote:

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 • 654 views
ADD COMMENTlink written 3.6 years ago by simonjean43410

Hello,

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

ADD REPLYlink written 14 months ago by sbbinfo900
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 249 users visited in the last hour