Motivation: Probes on an Affymetrix tiling array usually behave differently. Modeling and removing these probe effects are critical for detecting signals from the array data. Current data processing techniques either require control samples or use probe sequences to model probe-specific variability, such as with MAT. Although the MAT approach can be applied without control samples, it cannot remove probe effects completely.
Results: We propose TileProbe, a new technique that builds upon the MAT algorithm as well as publicly available data sets to remove tiling array probe effects. By using a large number of arrays existing in public database, TileProbe robustly models the residual probe effects that MAT model cannot explain. When applied to analyzing ChIP-chip data, TileProbe performs consistently better than MAT across a variety of analytical conditions. This shows that TileProbe resolves the issue of probe-specific effects more completely.
Supplementary Materials: Supplementary Figures and Tables
1. Download CisGenome (Linux or Mac OS) source code from here.
2. Unzip CisGenome:
> gzip –d *.gz
> tar xvf *.tar
3. Enter the CisGenome folder. Compile CisGenome by typing:
After compilation, in the “bin” folder, you will be able to find a series of programs tileprobe_*. These are the tileprobe executable files.
Usage (Command Line):
before you use TileProbe, you need to download BPMAP files from the MAT website and use those BPMAP files in the analysis.
Sample Parameter Files:
(1) MAT correction:
(2) Build model:
tileprobe_buildbarmodel_v2 -i trainlistov2.txt -o mousepromvBa
(3) Analyze new data step 1: MAT (the parameter file contains test data and has similar format to step (1) MAT correction)
(4) Analyze new data step 2: TileProbe correction
tileprobe_barnorm -i bMyc_1.bar -o . -m mousepromvBa
tileprobe_barnorm -i testlisto.txt -c 1 -o . -m mousepromvBa -b 0.0
(5) Analyze new data step 3: Peak detection
With IP and control:
TileProbe will be incorporated into CisGenome GUI shortly.
Precompiled Probe Models:
Affymetrix Mouse Promoter 1.0R: mm8
Affymetrix Mouse Tiling 2.0R: mm8
Affymetrix Human Promoter 1.0R: hg18