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Hi BioC users
I am working with affymetrix exon array data of 40 samples with 8
different groups and 5 replicates of each.
Two different strains are used in this study. Cells were cultured for
either 3 days or 7 days. At 3 days the cells are still proliferating
and are not considered mature , whereas at day 7 are considered as
mature. One of the 7 days cell cultures was treated with drug A and
another 7 days cell culture was treated with drug B for the entire
experiment. The remaining two cell cultures (3 and 7 days) were
remained untreated. One untreated cell culture was harvested after 3
days of growth, whilst the rest were harvested after 7 days of growth.
At the end of this experiment, there were 8 RNA samples: SV3, SV7,
SVA, SVB, BL3, BL7, BLA, and BLB . This procedure was repeated 5 times
to obtain 40 RNA samples in 8 groups.
Day 3
Treatment
Strain 1
Strain 2
Untreated pre-mature
SV3
BL3
Day 7
Untreated mature
SV7
BL7
Drug A treated mature
SVA
BLA
Drug B treated mature
SVB
BLB
*each has 5 replicates
I would like to compare the effect of different drug treatments on the
two strains with untreated samples i.e comparison of SV3, SV7, SVA and
SVB and BL3,BL7,BLA and BLB.
I am trying to create a design matrix for the complete data set, but
somehow I am mixing everything up. Can someone please help me with the
with the correct construction of the design matrix.
Best,
Sanjana
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