Assignment 4
1. Median Polish
a) Expression levels in four organs
Probe Leaf Root Panicle
Suspension_Cells
AGCAAAAATCATCAGCCTCTTCGTTACGATCGGTGA 212.22223 178.0 177.77777 161.88889
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b) Install R
c) Install Bioconductor
http://www.bioconductor.org/download
d) Use the median polish method from the affy package to do median polish.
> c <- matrix(, 3,2)
> c
[,1] [,2]
[1,]
NA NA
[2,]
NA NA
[3,]
NA NA
> c[,1]=c (0.1, 0.2, 0.4)
> c[,2]=c (0.5, 0.2, 0.4)
> c
[,1] [,2]
[1,] 0.1 0.5
[2,] 0.2 0.2
[3,] 0.4 0.4
> library(affy)
> medpolish(c, eps=0.01)
1 : 0.4
Final: 0.4
Median Polish Results (Dataset: "c")
Overall: 0.3
Row Effects:
[1] 0.0
-0.1 0.1
Column Effects:
[1] 0 0
Residuals:
[,1] [,2]
[1,] -0.2 0.2
[2,] 0.0 0.0
[3,] 0.0 0.0
2. Submit the expression matrix before and after median polish in separate files
Probe Leaf Root Panicle
Suspension_Cells
AGCAAAAATCATCAGCCTCTTCGTTACGATCGGTGA 212.22223 178.0 177.77777 161.88889
¡
a) Submit the files through eagle system
b) It is due at 11:59pm March 30.