---------- Forwarded message ----------
From: Asma rabe <asma.rabe@gmail.com>
Date: Wed, Oct 19, 2011 at 3:55 PM
Subject: edgeR questions
To: Bioconductor@r-project.org


Hi,

I've time course RNA-seq data that i would like to analyze using edgeR :

Q1) shall i normalize using calcNormFactors() or glmFit() and glmLRT() do
this normalization ,therefore no need to use calcNormFactors()??

Q2) when created design matrix using model.matrix(~mydata$samples$group) i
got a matrix in which the control has been removed ,i then calculates
dispersion using:

estimateGLMCommonDips(mydata,design matrix)

followed by testing using glmFit(),glmLRT()

Does the matrix created in a correct way?

Q3) In glmLRT() how can i determine the coefficient to be used if it is my
first time to analyze RNA-seq data??
Q4) After using glmFit(),glmLRT() followed by topTags() ,i got FDR =1 for
all genes,Any idea why FDR=1??

Thank you in advance.
Best Regards,
Rabe

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