Homework 3 due Oct 12
For the data on the web zipped as affyexamp.zip you are given 8 files. The result is from
a factorial design comparing the gender (M and F) and trt (N and T) with 2 replicates
each. The Target file and the descriptor file are also given for your interest. Please use
this data set to answer the following questions:
1.
2.
3.
4.
5.
6.
Provide the images for the 8 files.
Provide MA plots
Use a) MAS5 and b) RMA and c)GCRMAto normalize the affy-batch data.
Provide box-plots for the raw and normalized data.
How do the box-plots differ across the different normalization methods
If you were designing this study (where you had 8 zebrafish 4 males and 4 female
and trt with two levels) how would you go about it?
7. Are all three tenets of design (randomization, replication, blocking used in this
study).