[BioC] Help With RNA-seq

[Tina Asante Boahene]

Hi all,

I am conducting some analysis using the Marioni et al data.

However, I am having a bit of trouble using my data to conduct the analysis based on the baySeq package.

 And I was wondering if you could stir me in the right direction.

I have already used edgeR to find the library sizes for the ten libraries I have for my data as well as for the groups (Liver and Kidney) as stated below.


library(baySeq)
library(edgeR)
library(limma)
library(snow)

cl <- makeCluster(4, "SOCK")


##Calculating normalization factors##
D=MA.subsetA$M
head(D)
names(D)
dim(D)

g <- gsub("R[1-2]L[1-8]", "", colnames(D))
d <- DGEList(counts = D, group = substr(colnames(D), 5, 30))
d$samples
names(d)
dim(d)


I will like to know how to model my code in order to produce the MA plot for count data 


This is what I have, however it runs with the wrong response.

Can someone help me fix this please. 

CD <- new("countData", data = as.matrix(MA.subsetA$M), libsizes = as.integer(d$samples$lib.size))

plotMA.CD(CD, samplesA = 1:5, samplesB = 6:10, col = c(rep("red",
100), rep("black", 900)))


How can I get it to recognise the "groups" as "g" (Library and Kidney) 

This is the output for the groups   [1] "Kidney" "Liver"  "Kidney" "Liver"  "Liver"  "Kidney" "Liver"  "Kidney"  "Liver"  "Kidney"

thank you.






Kind Regards

Tina