Peng et al., BMC Bioinformatics (2007)

Please direct your questions to Peter J. Park.

All work was done in R; RData is the workspace that can be loaded into R directly. The code has not been fully annotated, but a proficient R programmer should be able to understand it easily.  Here, we provide the R code (28K) and  (5.25MB) to generate the key figures in the paper.

NimbleGen Data

The raw data are available in GEO (Series GSE8575)

To facilitate the data processing, we are also providing the "MA" data here (26Mb). M = log(R/G), and A = log(R*G)/2, where R and G are the intensities of the two-channels.

File description for MA data:

Column
Description
1
chromosome
2
probe location (start)
3
probe location (end)
4
M for MSL3-TAP (Embryos) replicate #1
5
A for MSL3-TAP (Embryos) replicate #1
6
M for MSL3-TAP (Embryos) replicate #1 (mock control)
7
A for MSL3-TAP (Embryos) replicate #1 (mock control)
8
M for MSL3-TAP (Embryos) replicate #2
9
A for MSL3-TAP (Embryos) replicate #2
10
M for MSL3-TAP (Embryos) replicate #2 (mock control)
11
A for MSL3-TAP (Embryos) replicate #2 (mock control)
NimbleGen Data: Probe Design File (NDF)16.56 MB