############################## # TileMap Parameter Settings # ############################## ############################## # Step O: Working Directory # ############################## O.1-[Working directory] = . O.2-[Project Title] = sample3 ############################## # Step I: Probe Summary # ############################## I.1-[Compute probe level test-statistics?] (1:yes; 0:no) = 0 #/* --------------------------------------------------- */ #/* If you choose "yes" in I.1, please prepare two */ #/* files in the working directory: */ #/* (i) The raw data file which contains the normalized */ #/* probe intensities. Provide its name in I.2 */ #/* (ii) A *.cmpinfo file named {Project Title}.cmpinfo */ #/* which specifies the hybridization pattern you */ #/* wish to select. */ #/* */ #/* If you choose "no" in I.1, please prepare a .txt */ #/* file that contains probe level test-statistics. */ #/* This file should have the same format as *.pbsum */ #/* files, and it will be used in Step II and Step III. */ #/* The probe level summary embedded in TileMap will be */ #/* skipped. */ #/* --------------------------------------------------- */ I.2-[Raw data file] = sample2_f_pb.sum #/* --------------------------------------------------- */ #/* Please specify the range of probe-level statistics. */ #/* */ #/* If you choose "yes" in I.1, you can set I.3 to */ #/* default. */ #/* */ #/* If you choose "no" in I.1, you should set I.3 */ #/* either to [0,1] or (-inf, +inf) depending on */ #/* whether the statistics in I.2 fall within */ #/* [0,1] (e.g. posterior probability) or (-inf, +inf) */ #/* (e.g. t-statistics. */ #/* */ #/* [0,1] statistics t will be transformed as */ #/* log[t/(1-t)] before applying MA, and the MA */ #/* statistics u will be transformed back by */ #/* exp(u)/[exp(u)+1] before applying UMS to estimate */ #/* local FDR. */ #/* */ #/* (-inf, +inf) statistics t will be transformed as */ #/* exp(t)/[exp(t)+1] before applying HMM. */ #/* --------------------------------------------------- */ I.3-[Range of test-statistics] (0: default; 1: [0,1], 2: (-inf, +inf)) = 1 #/* --------------------------------------------------- */ #/* To avoid logit(0), please specify */ #/* a zero cut in I.4. [0,1] test-statistics t will be */ #/* set to max(zero_cut/2, min(t, 1-zero_cut/2)). */ #/* before taking logit transformation. */ #/* */ #/* E.g. If [Monte Carlo draws for posterior prob.] in */ #/* *.cmpinfo file was set to 10000, you can set */ #/* zero_cut = 0.0001 (=1/10000). */ #/* --------------------------------------------------- */ I.4-[Zero cut] = 0.001 ############################## # Step II: Repeat Filtering # ############################## II.1-[Apply local repeat filter?] (0:No; 1:Yes) = 0 #/* --------------------------------------------------- */ #/* If you choose "yes" in II.1, please prepare a */ #/* *.refmask file which provides non-redundant probes */ #/* and counts repeat times of each probe. */ #/* Provide its name in II.2. This file will be used */ #/* as reference for masking local repeats. */ #/* */ #/* Hint: using tilemap_importaffy to load affymetrix */ #/* data will automatically create a *.refmask file. */ #/* */ #/* If you choose "no" in II.1, set II.2 to NULL. */ #/* Local repeat filtering will be skipped. */ #/* --------------------------------------------------- */ II.2-[*.refmask file] = NULL ############################## # Step III: Region Summary # ############################## III.1-[Combine neighboring probes?] (0:No; 1:Yes) = 1 III.2-[Method to combine neighboring probes] (0:HMM, 1:MA) = 0 #/* --------------------------------------------------- */ #/* If you choose "Yes" in III.1 and "HMM" in III.2, */ #/* please fill out Step IV and leave Step V to its */ #/* default values. */ #/* */ #/* If you choose "Yes" in III.1 and "MA" in III.2, */ #/* please fill out Step V and leave Step IV to its */ #/* default values. */ #/* */ #/* If you choose "No" in III.1, you can set III.2 */ #/* arbitrarily to 0 or 1 and leave both Step IV and */ #/* Step V to their default values. Region summary */ #/* will be skipped. */ #/* --------------------------------------------------- */ ############################## # Step IV: HMM # ############################## IV.1-[Posterior probability >] = 0.5 IV.2-[Maximal gap allowed] = 1000 IV.3-[Method to set HMM parameters] (0:UMS, 1:Set by users) = 0 #/* --------------------------------------------------- */ #/* If you choose "UMS" in IV.3, please set UMS */ #/* parameters in IV.4 - IV.10. */ #/* Otherwise leave them to be default values. */ #/* --------------------------------------------------- */ IV.4-[Provide your own selection statistics?] (0: No, use default; 1: Yes) = 1 IV.5-[If Yes to IV.4, selection statistics file] = sample2_f_pb.sum IV.6-[G0 Selection Criteria, p%] = 0.01 IV.7-[G1 Selection Criteria, q%] = 0.05 IV.8-[Selection Offset] = 1 IV.9-[Grid Size] = 1000 IV.10-[Expected hybridization length] = 28 #/* --------------------------------------------------- */ #/* If you choose "Set by users" in IV.3, please */ #/* provide your own transition, emission probability */ #/* matrices for HMM in IV.11 - IV.12. */ #/* Otherwise set them to NULL. */ #/* --------------------------------------------------- */ IV.11-[Path to transition probability matrix] = NULL IV.12-[Path to emission probability matrix] = NULL ############################## # Step V: Moving Average # ############################## V.1-[Local FDR <] = 0.5 V.2-[Maximal gap allowed] = 500 #/* --------------------------------------------------- */ #/* Set W -- the half window size -- in V.3. The */ #/* average will be taken over 2*W+1 contiguous probes */ #/* to compute MA statistic for the middle one. */ #/* --------------------------------------------------- */ V.3-[W] = 5 V.4-[Method to compute local FDR] (0:UMS; 1:Permutation Test) = 0 #/* --------------------------------------------------- */ #/* If you choose "UMS" in V.4, please set UMS */ #/* parameters in V.5 - V.10. */ #/* */ #/* If you choose "Permutation Test" in V.4, please */ #/* fill out V.10 to choose a grid size, and then go */ #/* back to {Project Title}.cmpinfo file and fill out */ #/* its "Permutation Setup" section. There you will set */ #/* how to do permutations and number of */ #/* permutations you want to do. */ #/* */ #/* Hint: depending on the size of the data, */ #/* permutation test could be very slow. */ #/* --------------------------------------------------- */ V.5-[Provide your own selection statistics?] (0: No, use default; 1: Yes) = 0 V.6-[If Yes to IV.4, selection statistics file] = NULL V.7-[G0 Selection Criteria, p%] = 0.01 V.8-[G1 Selection Criteria, q%] = 0.05 V.9-[Selection Offset] = 6 V.10-[Grid Size] = 1000