Entering edit mode
4.9 years ago
ecg1g15
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30
I am using the package maSigPro https://www.bioconductor.org/packages/devel/bioc/vignettes/maSigPro/inst/doc/maSigProUsersGuide.pdf to study the gene expression profiles over time I have a series of data with 7 timepoints and 1,2, or 3 replicates for each one.
>NBData
Time
Replicates
Group1
Group2
Group3
Sample1 0 1 1 0 0
Sample2 0 1 1 0 0
Sample3 1 2 1 0 0
Sample4 1 2 1 0 0
Sample5 1 2 1 0 0
Sample6 2 3 0 1 0
Sample7 2 3 0 1 0
Sample8 2 3 0 1 0
Sample9 3 4 0 1 0
Sample10 3 4 0 1 0
Sample11 4 5 0 1 0
Sample12 5 6 0 0 1
Sample13 5 6 0 0 1
Sample14 5 6 0 0 1
Sample15 6 7 0 0 1
Sample16 6 7 0 0 1
Sample17 6 7 0 0 1
Following the vignette for Next Generation-Sequencing series from the manual,
d <- make.design.matrix(NBdesign)
If we can use maSigPro with theta = 10:
library(MASS)
NBp <- p.vector(NBdata, d, counts=TRUE)
NBt <- T.fit(NBp)
I get the following error:
NBt <- T.fit(NBp, nvar.correction = FALSE)
[1] "fitting gene 100 out of 259"
[1] "fitting gene 200 out of 259"
Error in if (group != indepen) { : missing value where TRUE/FALSE needed
What does the error mean? is there a problem on my NBdata? or do I need any extra information on the T.fit function? Seems like the function started working fitting few genes and then brought up the error.
Thanks,