Hi,

I was wondering how to create my experimental design for my DESeq analysis

I have three conditions (ctrl, KO1 , KO2) of three type (I, NP, P) (total -
9 different comaprisons)

my phenoData file looks like that
SampleName    condition    libType
G1_I_C    ctrl    I
G1_I_KO1    KO1    I
G1_I_KO2    KO2    I
G1_NP_C    ctrl    NP
G1_NP_KO1    KO1    NP
G1_NP_KO2    KO2    NP
G1_P_C    ctrl    P
G1_P_KO1    KO1    P
G1_P_KO2    KO2    P
G2_I_C    ctrl    I
G2_I_KO1    KO1    I
G2_I_KO2    KO2    I
G2_NP_C    ctrl    NP
G2_NP_KO1    KO1    NP
G2_NP_KO2    KO2    NP
G2_P_C    ctrl    P
G2_P_KO1    KO1    P
G2_P_KO2    KO2    P
G3_I_C    ctrl    I
G3_I_KO1    KO1    I
G3_I_KO2    KO2    I
G3_NP_C    ctrl    NP
G3_NP_KO1    KO1    NP
G3_NP_KO2    KO2    NP
G3_P_C    ctrl    P
G3_P_KO1    KO1    P
G3_P_KO2    KO2    P

I would like to compare for each of the three lib_type the differentially
regulated genes between KO1/KO2 and the ctrl.

Is it possible to do a pair-wise comparison to see the differences in each
pair if I create a multifacotrial design matrix like that:

fit1 = fitNbinomGLMs( cdsFull, count ~ condition + libType )
fit0 = fitNbinomGLMs( cdsFull, count ~ condition )

or do I need to run each comparison separately like that:

res = nbinomTest( cds, group1, group2 )

where as group1 and group2 are each time the ctrl and KO1/KO2 for each
libType.


Thanks
Assa

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] RColorBrewer_1.0-5 genefilter_1.42.0  DESeq_1.12.1
lattice_0.20-24
[5] locfit_1.5-9.1     Biobase_2.20.1     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7
 [4] geneplotter_1.38.0   grid_3.0.1           IRanges_1.18.4
 [7] RSQLite_0.11.4       splines_3.0.1        stats4_3.0.1
[10] survival_2.37-4      tools_3.0.1          XML_3.95-0.2
[13] xtable_1.7-1

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