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Appendix D | Bayesian Robust Linear Model with Mahalanobis (BRLMM) Distance Classifier Al-
BRLMM RAM Requirements
The most common challenge for users running BRLMM is the amount
of RAM available for analytical processes. When BRLMM performs an
analytical function, it attempts to split up each operation into the
amount of RAM that appears free on your computer. Operations are
split by subdividing the analysis into blocks of probesets (or SNPs).
Small blocks of probesets subdivide the operation even more, but
require less memory at the expense of having to read the CEL files
more frequently. On the other hand, if you use a smaller number of
large blocks of probesets, it requires more memory, but places
minimal load on reading the CEL files.
The default behavior for BRLMM is to estimate the optimal block size
based upon the amount of memory that appears to be free at the time
the job begins. This default behavior can be overridden by the user
with the use of the
--block-size option
that specifies the number of
probesets to be processed at one time. For example, specifying
--block-
size=20000
analyzes data in batches of 20,000 probesets at a time.
Table D.2
BRLMM parameter settings
Parameter
Default Value
Description
Score Threshold
0.5
Maximum score (i.e. lowest
confidence) at which to make a call, all
calls of lower confidence get no call.
BlockSize
0
How many probe sets to process at
one time; useful when memory is
limited. If set to 0, the program
attempts to guess available RAM and
sets appropriately.
PriorSize
10000
How many probe sets to use for
determining prior.
DMThreshold
0.17
DM confidence threshold used for
seeding clusters.
GTYPE_manual.book Page 373 Wednesday, August 2, 2006 11:31 AM
Содержание iServer MicroServer iTHX-M
Страница 9: ...Introduction GTYPE_manual book Page 1 Wednesday August 2 2006 11 31 AM...
Страница 10: ...GTYPE_manual book Page 2 Wednesday August 2 2006 11 31 AM...
Страница 19: ...Chapter 1 GTYPE Overview GTYPE_manual book Page 11 Wednesday August 2 2006 11 31 AM...
Страница 20: ...Chapter 1 GTYPE_manual book Page 12 Wednesday August 2 2006 11 31 AM...
Страница 55: ...Chapter 2 Getting Started GTYPE_manual book Page 47 Wednesday August 2 2006 11 31 AM...
Страница 56: ...Chapter 2 GTYPE_manual book Page 48 Wednesday August 2 2006 11 31 AM...
Страница 85: ...Chapter 3 Working with Images GTYPE_manual book Page 77 Wednesday August 2 2006 11 31 AM...
Страница 86: ...Chapter 3 GTYPE_manual book Page 78 Wednesday August 2 2006 11 31 AM...
Страница 113: ...Chapter 4 Analyzing Cell Intensity Data GTYPE_manual book Page 105 Wednesday August 2 2006 11 31 AM...
Страница 114: ...Chapter 4 GTYPE_manual book Page 106 Wednesday August 2 2006 11 31 AM...
Страница 145: ...Chapter 5 Mapping Analysis Window GTYPE_manual book Page 137 Wednesday August 2 2006 11 31 AM...
Страница 146: ...Chapter 5 GTYPE_manual book Page 138 Wednesday August 2 2006 11 31 AM...
Страница 187: ...Chapter 6 Working with Mapping Data GTYPE_manual book Page 179 Wednesday August 2 2006 11 31 AM...
Страница 188: ...Chapter 6 GTYPE_manual book Page 180 Wednesday August 2 2006 11 31 AM...
Страница 259: ...Chapter 7 Universal Tag Window GTYPE_manual book Page 251 Wednesday August 2 2006 11 31 AM...
Страница 260: ...Chapter 7 GTYPE_manual book Page 252 Wednesday August 2 2006 11 31 AM...
Страница 269: ...Chapter 8 Probe Intensity Window GTYPE_manual book Page 261 Wednesday August 2 2006 11 31 AM...
Страница 270: ...Chapter 8 GTYPE_manual book Page 262 Wednesday August 2 2006 11 31 AM...
Страница 283: ...Chapter 9 NetAffx Annotations GTYPE_manual book Page 275 Wednesday August 2 2006 11 31 AM...
Страница 284: ...Chapter 9 GTYPE_manual book Page 276 Wednesday August 2 2006 11 31 AM...
Страница 297: ...Chapter 10 Reports GTYPE_manual book Page 289 Wednesday August 2 2006 11 31 AM...
Страница 298: ...Chapter 10 GTYPE_manual book Page 290 Wednesday August 2 2006 11 31 AM...
Страница 313: ...Appendix A Installing GTYPE Software GTYPE_manual book Page 305 Wednesday August 2 2006 11 31 AM...
Страница 314: ...Appendix A GTYPE_manual book Page 306 Wednesday August 2 2006 11 31 AM...
Страница 325: ...Appendix B MPAM Mapping Algorithm GTYPE_manual book Page 317 Wednesday August 2 2006 11 31 AM...
Страница 326: ...Appendix B GTYPE_manual book Page 318 Wednesday August 2 2006 11 31 AM...
Страница 343: ...Appendix C Dynamic Model Mapping Algorithm GTYPE_manual book Page 335 Wednesday August 2 2006 11 31 AM...
Страница 344: ...Appendix C GTYPE_manual book Page 336 Wednesday August 2 2006 11 31 AM...
Страница 362: ...Appendix D GTYPE_manual book Page 354 Wednesday August 2 2006 11 31 AM...
Страница 385: ...Appendix E Mapping Tool Algorithms GTYPE_manual book Page 377 Wednesday August 2 2006 11 31 AM...
Страница 386: ...Appendix E GTYPE_manual book Page 378 Wednesday August 2 2006 11 31 AM...
Страница 393: ...Appendix F IUPAC Base Codes GTYPE_manual book Page 385 Wednesday August 2 2006 11 31 AM...
Страница 394: ...Appendix F GTYPE_manual book Page 386 Wednesday August 2 2006 11 31 AM...
Страница 397: ...Appendix G File Types GTYPE_manual book Page 389 Wednesday August 2 2006 11 31 AM...
Страница 398: ...Appendix G GTYPE_manual book Page 390 Wednesday August 2 2006 11 31 AM...
Страница 401: ...Appendix H Working with Windowpanes Columns GTYPE_manual book Page 393 Wednesday August 2 2006 11 31 AM...
Страница 402: ...Appendix H GTYPE_manual book Page 394 Wednesday August 2 2006 11 31 AM...
Страница 405: ...Appendix I Hot Key Descriptions GTYPE_manual book Page 397 Wednesday August 2 2006 11 31 AM...
Страница 406: ...Appendix I GTYPE_manual book Page 398 Wednesday August 2 2006 11 31 AM...
Страница 409: ...Index GTYPE_manual book Page 401 Wednesday August 2 2006 11 31 AM...
Страница 410: ...GTYPE_manual book Page 402 Wednesday August 2 2006 11 31 AM...