Question: Setting up design matrix in Limma
gravatar for sanj
6.6 years ago by
United Kingdom
sanj20 wrote:
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 [[alternative HTML version deleted]]
sva • 537 views
ADD COMMENTlink written 6.6 years ago by sanj20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 284 users visited in the last hour