Changeset 791
- Timestamp:
- Sep 24, 2008, 9:16:08 PM (14 years ago)
- Location:
- plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror
- Files:
-
- 3 edited
Legend:
- Unmodified
- Added
- Removed
-
plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/AcrossAssays/ReplicateErrorAA.java
r784 r791 209 209 210 210 Iterator<String> it = groups.keySet().iterator(); 211 PrintStream groupsFile = new PrintStream(new File("data", "groups.data"));212 211 while (it.hasNext()) 213 212 { … … 222 221 else 223 222 { 224 groupsFile.println(key);225 223 HTML.addGroup(key, assayIdToName(group)); 226 224 } … … 325 323 } 326 324 327 Iterator<Integer> i = replicates.keySet().iterator(); 328 while (i.hasNext()) 329 { 330 Integer reporter = i.next(); 331 Replicate r = replicates.get(reporter); 332 if (r.valid()) 333 { 334 Iterator<Spot[]> dupI = r.duplicateIterator(); 335 while (dupI.hasNext()) 336 { 337 Spot[] d = dupI.next(); 338 R.replica1Range(d[0].getM()); 339 R.replica2Range(d[1].getM()); 340 R.replicaMRange(Replicate.getReplicateM(d[0], d[1])); 341 } 342 } 343 else 344 { 345 i.remove(); 346 if (leaveSingletons && r.size() == 1) 347 { 348 singletons.put(reporter, r); 349 } 350 } 351 } 325 // remove unusable replicates 326 purgeUnusableReplicates(replicates, singletons); 352 327 353 328 // calculate mean or median befor filter … … 368 343 R.setABRBefore(groupName, caluculateABR(replicates.values())); 369 344 370 // print result 345 // print result to file for later use in R 371 346 printDuplicates(replicates.values(), groupName + ".data"); 372 347 … … 376 351 r.filter(averageBefore, sdLimit * sdBefore); 377 352 } 353 // print result to file for later use in R 378 354 printDuplicates(replicates.values(), groupName + "good.data"); 379 355 -
plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/ReplicateError.java
r784 r791 241 241 } 242 242 243 protected void purgeUnusableReplicates(HashMap<Integer, Replicate> replicates, 244 HashMap<Integer, Replicate> singletons) 245 { 246 Iterator<Integer> i = replicates.keySet().iterator(); 247 while (i.hasNext()) 248 { 249 Integer reporter = i.next(); 250 Replicate r = replicates.get(reporter); 251 if (r.valid()) 252 { 253 Iterator<Spot[]> dupI = r.duplicateIterator(); 254 while (dupI.hasNext()) 255 { 256 Spot[] d = dupI.next(); 257 R.replica1Range(d[0].getM()); 258 R.replica2Range(d[1].getM()); 259 R.replicaMRange(Replicate.getReplicateM(d[0], d[1])); 260 } 261 } 262 else 263 { 264 i.remove(); 265 if (leaveSingletons && r.size() == 1) singletons.put(reporter, r); 266 } 267 } 268 } 269 243 270 protected List<Float> getMList(Collection<Replicate> replicates) 244 271 { -
plugins/base1/se.lu.onk.ReplicateError/trunk/src/replicateerror/WithinAssays/ReplicateErrorWA.java
r784 r791 61 61 { 62 62 HTML.openGroup(); 63 PrintStream groupsFile = new PrintStream(new File("data", "groups.data"));64 63 String[] vals; 65 64 while ((vals = bfr.readDataRow()) != null) 66 65 { 67 66 assayName.put(new Integer(vals[idCol]), vals[nameCol]); 68 groupsFile.println(vals[nameCol]);69 67 } 70 groupsFile.close();71 68 HTML.closeGroup(); 72 69 } … … 139 136 140 137 // remove unusable replicates 141 Iterator<Integer> it = replicates.keySet().iterator(); 142 while (it.hasNext()) 143 { 144 Integer reporter = it.next(); 145 Replicate r = replicates.get(reporter); 146 if (leaveSingletons && r.size() == 1) 147 { 148 singletons.put(reporter, r); 149 it.remove(); 150 } 151 else 152 { 153 Iterator<Spot[]> dupI = r.duplicateIterator(); 154 while (dupI.hasNext()) 155 { 156 Spot[] d = dupI.next(); 157 R.replica1Range(d[0].getM()); 158 R.replica2Range(d[1].getM()); 159 R.replicaMRange(Replicate.getReplicateM(d[0], d[1])); 160 } 161 } 162 } 138 purgeUnusableReplicates(replicates, singletons); 163 139 164 140 int nbrBefore = replicates.size(); … … 180 156 R.setABRBefore(assayName.get(assay), caluculateABR(replicates.values())); 181 157 182 // print result 158 // print result to file for later use in R 183 159 printDuplicates(replicates.values(), assayName.get(assay) + ".data"); 184 160 … … 188 164 r.filter(averageBefore, sdLimit * sdBefore); 189 165 } 166 // print result to file for later use in R 190 167 printDuplicates(replicates.values(), assayName.get(assay) + "good.data"); 191 168
Note: See TracChangeset
for help on using the changeset viewer.