Designed for use with Apache Ant.
| 2006-08-17 20:06 jwang |
Updated keystore with new self-signed certificate valid for 360 days. Signed all jars in vendor/lib. |
| 2006-08-17 20:06 jwang |
Updated keystore with new self-signed certificate valid for 360 days. Signed all jars in vendor/lib.
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| 2006-08-17 16:26 vinodh |
Removed System.out debugging messages
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| 2006-08-16 15:11 vinodh |
Removed System.out debugging messages.
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| 2006-08-16 00:14 jwang |
Relaxed the delta slightly for variance assert(). |
| 2006-08-15 21:21 jwang |
Added another patch to 'Fs + permutation test' range-checking related unit tests. This needs more thought. |
| 2006-08-15 21:19 jwang |
Added workaround for bug #95, the subtitles for groups with large numbers of arrays were crowding out the actual plot. See details at http://bugs.ssg.uab.edu/bugzilla/show_bug.cgi?id=95. |
| 2006-08-15 16:16 jwang |
Updated unit test to use CRLF as the line separator to be consistent with the newly updated behavior (to use \r\n regardless of platform) of the 'MS Excel CSV' printer. |
| 2006-08-15 03:09 jwang |
Minor update to 'two group analysis' workflow so that 'deleted residuals' can be requested by itself without having to specify a test of hypothesis for a single run. Minor whitespace cleanup for readability. |
| 2006-08-15 02:51 jwang |
Updated unit test expected value for a particular assert() that is failing frequently within 25% delta. The previous value appears to be further than +/- delta away from the true parameter although further thought is needed to establish a better estimate for that parameter. Right now we are using an rbitrarily chosen previous estimate as the expected value. |
| 2006-08-15 01:33 jwang |
Widen range of acceptable p-values for a particular test case. Probably need to think about this more thoroughly. |
| 2006-08-14 21:32 jwang |
Updated to use CRLF as the line terminator instead of asking for the platform-dependent 'line separator' property. This was done to facilitate testing across platforms, but the overall impact of this change is a topic of continuing research. |
| 2006-08-14 21:18 jwang |
Fixed estimates.object and unit test so that it works under Java 1.4 (it was originally committed under Java 1.5, but because we don't yet use that version in production, we needed to fix this serialization error). |
| 2006-08-11 14:56 jwang |
Added test case to the 'robust N-way ANOVA' unit test to verify that the ANOVA degenerates to a equal variance t-test when a group is completely missing (in the 3-group case). Added toString() implementation to TTest. |
| 2006-08-11 14:42 jwang |
Updated 'residual statistics' class to use the 'class' classloader instead of the 'system' classload so that it works under both Java Web Start and in the development environment. Updated the unit test for the older K-S test to accomodate the newer API in the 'residual statistics' class. |
| 2006-08-10 20:38 jwang |
Upgraded to use the classloader that loads the class rather than the system classloader to work more generally. The previous call used the system classloader, this worked for builds on the desktop, but not through Java Web Start (for hopefully obvious reasons). |
| 2006-08-10 20:36 jwang |
Upgraded build status to beta and incremented build number. |
| 2006-08-10 19:53 jwang |
branches: 1.1.2; file TestNormativePValue.java was initially added on branch RB_1_5. |
| 2006-08-10 19:53 jwang |
branches: 1.1.2; file NormativePValue.java was initially added on branch RB_1_5. |
| 2006-08-10 19:53 jwang |
Added first pass at support (including spec reviewed by Grier) for normative QC in deleted residuals and K-S D statistics. Added normative p-value class and unit test. Added K-S D statistics calculated for each microarray in the GEO database to resources. Integrated normative QC support into existing 'residual statistics' classes, though this glue code needs heavy refactoring in the hopefully not-too-distant future.
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| 2006-08-10 19:53 jwang |
branches: 1.1.2; file ks_from_geo.txt was initially added on branch RB_1_5. |
| 2006-08-08 19:58 jwang |
Updated handling for completely missing data for a Y vector. Updated unit test to handle a few more degenerate cases. |
| 2006-08-02 21:38 jwang |
Added unit test case to exercise the fix for bug #143 at http://bugs.ssg.uab.edu/bugzilla/show_bug.cgi?id=143. |
| 2006-08-02 21:38 jwang |
branches: 1.3.2; Added unit test case to exercise the fix for bug #143 at http://bugs.ssg.uab.edu/bugzilla/show_bug.cgi?id=143. |
| 2006-08-02 16:47 jwang |
Added another dataset to test missing values support in 'robust' N-way ANOVA implementation. |
| 2006-08-01 22:04 jwang |
Fixed to compile under Java 1.4.2. |
| 2006-08-01 21:19 jwang |
Minor whitespace and exception message tweaks for readability and consistency. |
| 2006-08-01 20:55 jwang |
branches: 1.1.2; Added first pass at better handling of missing values in the Y vector for the ANOVA analysis workflow. Refactored related unit test classes to test each implementation of the 'n-way ANOVA' concept completely, not just the 'fast' implementation. There may be a cleaner design to be had using the JUnit concept of a 'test suite'. |
| 2006-08-01 20:55 jwang |
Added first pass at better handling of missing values in the Y vector for the ANOVA analysis workflow. Refactored related unit test classes to test each implementation of the 'n-way ANOVA' concept completely, not just the 'fast' implementation. There may be a cleaner design to be had using the JUnit concept of a 'test suite'.
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| 2006-08-01 15:18 jwang |
Updated URL in javadoc comments to point to the bugs.ssg.uab.edu CNAME record instead of a hard-coded IP address. |
| 2006-07-26 03:25 jwang |
Added reference to PNAS paper describing deleted residuals and K-S test to javadoc comments. |
| 2006-07-24 22:24 jwang |
branches: 1.4.2; Added first pass at support for newly refactored Kolmogorov-Smirnov test API for the 'quality control' package. |
| 2006-07-24 22:24 jwang |
Added first pass at support for newly refactored Kolmogorov-Smirnov test API for the 'quality control' package. |
| 2006-07-20 22:18 jwang |
Added first pass at newly-redesigned 'deleted residuals' API. This resdesign decouples this class from other classes in the data model and is more flexible in its minimalism. Added unit test. |
| 2006-07-11 22:19 jwang |
Updated charts in newer power code to dynamically adjust the range of the logarithmic axis, instead of just hard-coding the upper range to 200, which obviously makes for some funny-looking charts when the user supplies different values for the sample sizes.
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| 2006-07-10 15:18 vinodh |
HTMLReport is no longer used to generate Summary HTML Report |
| 2006-07-10 15:02 vinodh |
branches: 1.62.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
Merging branch RFE_142
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| 2006-07-10 15:02 vinodh |
branches: 1.12.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.20.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.39.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.30.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.5.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.42.2; Merging branch RFE_142 |
| 2006-07-10 15:02 vinodh |
branches: 1.31.2; Merging branch RFE_142 |
| 2006-07-04 20:30 ssg |
Changed reports directory names |
| 2006-07-04 02:41 vinodh |
AnovaHTMLReport class is removed and is not responsible for the creation of Anova HTML Summary report. |
| 2006-07-04 02:39 vinodh |
HTMLReport class removed and is no longer responsible for the creation of HTML Summary report. |
| 2006-07-03 19:56 vinodh |
branches: 1.1.2; required for HDBStat! 1.3+ |
| 2006-07-02 03:41 jwang |
Added reference to related RFE, http://bugs.ssg.uab.edu/bugzilla/show_bug.cgi?id=140. |
| 2006-06-30 20:17 vinodh |
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| 2006-06-30 19:59 vinodh |
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| 2006-06-30 19:53 vinodh |
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| 2006-06-30 19:47 vinodh |
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| 2006-06-30 19:47 vinodh |
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| 2006-06-30 19:46 vinodh |
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| 2006-06-30 19:46 vinodh |
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| 2006-06-30 19:44 vinodh |
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| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file anovaCompendiumReport.vm was initially added on branch RFE_142. |
| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file modifiedAnovaReport.vm was initially added on branch RFE_142. |
| 2006-06-30 19:17 vinodh |
Compendium related changes
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| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file ChipLevelInfoCsvWriter.java was initially added on branch RFE_142. |
| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file compendiumReadme.vm was initially added on branch RFE_142. |
| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file twogroupCompendiumReport.vm was initially added on branch RFE_142. |
| 2006-06-30 19:17 vinodh |
branches: 1.1.2; file enhancedHdbstatReport.vm was initially added on branch RFE_142. |
| 2006-06-29 23:21 jwang |
branches: 1.3.2; Minor tweak to stream closing code, in this case, we don't want to close the stream to allow the client the flexibility of writing additional bytes (say, if they are creating a zip file) at the expense of putting the burden of closing on the client-side. |
| 2006-06-29 23:21 jwang |
Minor tweak to stream closing code, in this case, we don't want to close the stream to allow the client the flexibility of writing additional bytes (say, if they are creating a zip file) at the expense of putting the burden of closing on the client-side. |
| 2006-06-29 23:07 jwang |
Added standard error for TP, TN, and EDR to table. This is a temporary patch ahead of plans to go ahead and output the 95% CI. Most users will know how to get to a confidence interval given the point estimate and the standard error. Updated md5sum. |
| 2006-06-29 22:57 jwang |
Removed old, unused, and ill-conceived class. |
| 2006-06-29 22:52 jwang |
branches: 1.1.2; Added first pass at table for new power analysis code. Added unit test. Added md5sum class to utility package. |
| 2006-06-29 22:52 jwang |
Added first pass at table for new power analysis code. Added unit test. Added md5sum class to utility package. |
| 2006-06-22 02:02 jwang |
Added fix and unit test for bug #153 at http://bugs.ssg.uab.edu/bugzilla/show_bug.cgi?id=153. |
| 2006-06-06 20:45 jwang |
Updated Estimator.Estimate class with more accessors, including toString(), and added the Serializable marker interface to support the intended usage. Added first pass at refactoring and visually tweaking the 'power analysis'-related plots from the Power Atlas and merging them into the newly written 'power analysis' code.
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| 2006-06-05 20:05 jwang |
Updated CD4 test case with the corrected values for lambda0, r, and s. The results now match exactly with Dr. Gadbury's table from S-Plus for the paper. |
| 2006-06-02 20:16 jwang |
Renamed MixomaticEstimator class to Estimator. Renamed MixomaticModel class to OptimizationModel for clearer semantics. Updated unit tests.
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| 2006-06-02 19:23 jwang |
Renamed PowerEstimator class to Estimator. Updated unit test. |
| 2006-06-02 19:14 jwang |
Added 'standard error' getter for the TP, TN, and EDR estimates. Updated unit test assert() deltas to use the standard error, which is more sensible then using an arbitrary 1% percent delta. |
| 2006-06-01 19:41 jwang |
Added first pass at support for 'equivalent' equal group sample size, for situations where N1 and N2 are not the same. Added rudimentary test case. |