# If the experiment contains two groups (e.g., IP vs. Input from Affymetrix arrays), Comparison Type = 2.
# You will assign group ids 1 and 2 to arrays, and the pattern you will look for is something like 1>2.
# If the experiment contains only one group (e.g., log2(IP/Input) from NimbleGen or Agilent arrays), Comparison Type = 1.
# You will only assign group id 1 to arrays, and the pattern you will look for is 1>0.0.
# If the experiment contains more than two groups, Comparison Type = 3.
# You are looking for patterns like (1>2) & (3>4), etc.
[Comparison Type] (1: One Sample; 2: Two Sample; 3: Multiple Sample) = 2

# The folder to export analysis results
[Working Directory] = C:\Users\jihk\rest\analysis\

# The file title used to export analysis results. Results will be saved to several files with a name starting with your file title
[Project Title] = restpeak_affy

# How many array types do you have. For example, Affymetrix Human Tiling 2.0R contains 7 different arrays, so the No. of Library = 7.
# Affymetrix Human promoter array contains only one array, so No. of Library = 1.   
[No. of Libraries] = 7

# How many samples do you have. For Affymetrix data, this is equal to No. of IP samples + No. of Control samples. 
# For NimbleGen or Agilent, this is equal to No. of IP/Control pairs (since each array produce a log2(IP/Input) ratio).
[No. of Samples] = 4

# How many groupd do you have. Should be consistent with [Comparison Type].
[No. of Groups] = 2

# Normalized data files in BAR file formats. Each sample starts with a line [N]->[Alias].
# [N]->[Alias]: N is the group id. Alias is the name for the sample. 
# Following [N]->[Alias] are [M] lines that contain array file names, where M is the No. of libraries. Files should be ordered according to 
# the order of libraries
[Data]
1->IP1
Johnson_IP364AMP(120506)_Hs35b_P01R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P02R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P03R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P04R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P05R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P06R_v01.CEL.bar
Johnson_IP364AMP(120506)_Hs35b_P07R_v01.CEL.bar
1->IP2
Johnson_IP369AMP(120506)_Hs35b_P01R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P02R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P03R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P04R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P05R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P06R_v01.CEL.bar
Johnson_IP369AMP(120506)_Hs35b_P07R_v01.CEL.bar
2->CT1
Johnson_Jurkat-Mock-10(091806)_Hs35b_P01R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P02R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P03R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P04R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P05R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P06R_v01.CEL.bar
Johnson_Jurkat-Mock-10(091806)_Hs35b_P07R_v01.CEL.bar
2->CT2
Johnson_Jurkat-Mock-7(091806)_Hs35b_P01R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)_Hs35b_P02R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)_Hs35b_P03R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)-Rerun_Hs35b_P04R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)_Hs35b_P05R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)_Hs35b_P06R_v01.CEL.bar
Johnson_Jurkat-Mock-7(091806)_Hs35b_P07R_v01.CEL.bar

# The peak pattern you are looking for. For example, in a two sample comparison, you have two groups: 1=IP, 2=control, 
# you want to find pattern 1>2 as your peak; in a one sample comparison, you have only one group, 1=log2(IP/Input), 
# you want to find pattern 1>0.0 as your peak; in multiple sample comparisons, you have >2 groups, 1=tissue1, 2=tissu2, 3=tissue3,
# you want to find pattern 1>2 & 1>3 as your peak. 
[Patterns of Interest]
1>2

# Affymetrix CEL file contains a section called "Outliers". If you want to exclude these outlier probes from the analysis, 
# you should do two things. First, when running tilemapv2_importaffy, set [Remove outlier cells in the CEL files] = 1. Second, 
# in this file, set [Masking Bad Data Points] = 1. 
[Masking Bad Data Points] (0:No, 1:Yes) = 0

# If your data in the bar files have not been log2 transformed, you want to log transform them. So you want to first truncate everything
# smaller than zero to a small positive value, and then take log. Truncation lower bound is the small positive value you choose. 
# If your data have already been log transformed in tilemapv2_importaffy, then you don't need to tranform them again, so you want to set
# the truncation lower bound to be a very negative number, and truncation upper bound to be a very positive number. As a result, nothing
# will change to your data which are usually in the range of 5-15 after log2 transformation.
# Example: if [Truncation Lower Bound] = 1, [Truncation Upper Bound] = 100000, [Transformation] = 1, then your data x will be transformed 
# as follows: y = log2{ min[ max(1,x), 100000 ] } 
[Truncation Lower Bound] = -1000000.000000
[Truncation Upper Bound] = 1000000.000000
[Transformation] (0: Identity; 1: log2; 2: logit; 3: exp(x)/1+exp(x)) = 0

# You have N groups set by [No. of Groups]. If you assume that for each probe, the within-group variance is the same for all groups,
# then the no. of common variance group is 1. You will set [Common Variance Groups] = 1, and using a single line to include all group ids
# to tell the program that all groups have the common variance.
# If you assume that the within group variance is not the same for all groups, then you need to specify which groups are assumed to have 
# common variance. For example, if you have 3 groups with group id 1, 2 and 3, and if you assume that group 1 and 2 have the same variance
# but group 3 has a different variance, then  [Common Variance Groups] = 2, and this will be followed by two lines, one line is "1 2", and
# the other line is "3".
[Common Variance Groups] = 1
1 2

# Which method to use to combine neighboring probes
[Method to Combine Neighboring Probes] (0:HMM, 1:MA) = 1

# which method to use to compute FDR. Usually = 0.
[Method to Compute FDR] (0: Estimate from Left Tail; 1: Permutation Test; 2: UMS; 3: No FDR) = 0

# half window size, i.e. 2*W+1 probes will be used to derive MA statistic
[W] = 5

# half window size in terms of the number of base pairs. Ideally 2*W+1 probes will be used to compute MA, however, if any probe is located
# too far away (i.e. further than the window boundary), then the probe will be excluded from MA computation. As a result, the MA
# statistic for the centering probe will be based on fewer than 2*W+1 probes. 
[Window Boundary] = 300

# "=1" usually recommended
[Standardize MA Statistics] (0:No; 1:Yes) = 1

# MA cutoff. Probes with MA statistic >= this cutoff will be used to form peaks.
[Region Boundary Cutoff, MA>] = 3.000000

# How many probes are expected to be covered by an average peak
[Expected Hybridization Length] = 28

# HMM cutoff
[Posterior Probability Cutoff, P>] = 0.500000

# p and q for UMS computation. Please refer to the original TileMap paper.
[G0 Selection Criteria, p%] = 0.010000
[G1 Selection Criteria, q%] = 0.050000

# in HMM, offset = 1; in MA offset = W+1
[Selection Offset] = 6

# how many bins to group the probes in UMS. Please refer to the original TileMap paper.
[Grid Size] = 1000

# If permutation is used to compute FDR, how many permutations to use
[Number of Permutations] = 10

# If permutation is used to compute FDR, which groups are assumed to be exchangeable. Array labels will be permuted within exchangable 
# groups. [Exchangeable Groups] is the number of exchangeable groups, and this line is followed by lines that specify which group ids are 
# included in each exchangeable group.
[Exchangeable Groups] = 1
1 2

# Two peaks with distance < Max Gap will be merged.
[Max Gap within a Region] = 300

# If a peak contain [Max Run] continuous probes that do not pass the significance cutoff, it will be broken into two peaks.
[Max Run of Insignificant Probes within a Region] = 5

# Min length of a peak. Peaks shorter than this will not be reported.
[Min Region Length] = 100

# Min number of probes passing the significance cutoff. If a peak contains < [Min No. of Significant] probes that pass the cutoff, it
# will not be reported.
[Min No. of Significant Probes within a Region] = 5