Dear All,

I have some queries regarding design matrix for two group(Control vs. KO)
Differential expression.I am using edgeR for this. Here is the ording of my
question:- 1) Sample table for design matrix, 2) Design matrix, 3)
Questions.

*1) Sample table for design matrix*

     Sample                 Strain                    Condition

     KO1-A                   1                              KO

     KO1-B                   1                              KO

     KO2-A                   2                              KO

     KO2-B                   2                              KO

     Cont1-A               1                              Control

     Cont1-B                1                              Control

     Cont2-A               2                              Control

     Cont2-B                2                              Control


*2) Design Matrix*


targets <- read.table(file= "Samples",sep="\t",header=TRUE)

design <- model.matrix(~Strain+Condition,targets)

> design

          (Intercept) Strain ConditionKO

KO1-A           1      1           1

KO1-B           1      1           1

KO2-A           1      2           1

KO2-B           1      2           1

Cont1-A           1      3           0

Cont1-B           1      3           0

Cont2-A           1      4           0

Cont2-B           1      4           0

attr(,"assign")

[1] 0 1 2

attr(,"contrasts")

attr(,"contrasts")$Condition

[1] "contr.treatment"


*3) Questions*

1)      *A)* During differential expression I also want to consider
different strain variation along with the control vs KO variation.  As far
as I understand this design matrix only consider one Control vs KO for DE.
I would like to known How I can make it consider strain variation as well?

2)      *B)* After DE using the same design matrix with glmFit, I inspect
the read count for the top down regulated gene and find out that the read
count for this gene is very low in knockout as compare to Control . So is
it means the comparison is Control vs KO and topTags gives the DEG list in
KO as compare to Control?
I would appreciate your suggestion.

Kind Regards


-- 
Reema Singh
Postdoctoral Research Assistant
College of Life Sciences
University of Dundee,
Dundee DD1 4HN, Scotland
United Kingdom

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