90f4da8ebac1418098f4a926943e468a *DESCRIPTION
8b1ecca81c7b61b2307ec62aac27b74a *NAMESPACE
9400b3c4ffcd01c344a61387d7131750 *R/000.R
646155cdee987c9e73189073bc88c53b *R/006.fixVarArgs.R
dc193ab3c1d3cf0b5cd9400752585fa5 *R/009.setup.R
94bf454cc3e6953b6feb80599602b47e *R/999.AromaAffymetrix.R
dcb0e44d79e9859ee6006eb8c70b2837 *R/999.NonDocumentedObjects.R
dddb2f475fa0f1449c51432820791270 *R/999.package.R
6af401f75860403b7ef1bec61a5e49b5 *R/ASCRMAv2.R
0f6664c7a9f946dc87993c7c8dc7539f *R/AbstractProbeSequenceNormalization.R
34dc273926fb7f6c7285211aa48e67cf *R/AdditiveCovariatesNormalization.R
8b0fddb84eef1b785aa7c6a692163fe7 *R/AffineCnPlm.R
7a12ae7b1781e411bc0a26b5457a16b5 *R/AffinePlm.R
daedbc980d84a07b3e2638afccea9d18 *R/AffineSnpPlm.R
0965e981a66502e389ad86b7125ab711 *R/AffyGenePDInfo.writeCdf.R
5cc48e097748271e5c1f712c162ee994 *R/AffymetrixAptSummaryFile.R
90ed2f05080d30626ee1dc0a0d5c25c5 *R/AffymetrixCdfFile.COUNTS.R
f2a56ee9e7df886a7e6dd63af2f34a70 *R/AffymetrixCdfFile.MONOCELL.R
dc999943de6ac6744321ac90c64221c1 *R/AffymetrixCdfFile.PLOT.R
4534027dfee633804750b402700b7660 *R/AffymetrixCdfFile.R
db5a7bec2414dbe878dc3505ec835ca8 *R/AffymetrixCdfFile.SNPs.R
6989b10dc1b36c7eac5537cc7328dfce *R/AffymetrixCdfFile.UNIQUE.R
60d503c047fa22fd8487031693a94f50 *R/AffymetrixCdfFile.computeAffinities.R
07e1d5dd7a07d319cc3aafc3c10e026a *R/AffymetrixCdfFile.getAlleleCellPairs.R
c7ecf3244a2e6f7a2e70c5b2d06334f2 *R/AffymetrixCdfFile.getAlleleProbePairs.R
d7f2c37c676d63fcb3d6f993b8b6c385 *R/AffymetrixCdfFile.getAlleleProbePairs2.R
76874efcc662c6c92440c6ec2913853b *R/AffymetrixCdfFile.getAlleleProbePairs3.R
41066c087747b4e02e8664d8d28df948 *R/AffymetrixCdfFile.getCellQuartets.R
a20efaba313139084c1a5eb860e2a1c9 *R/AffymetrixCdfFile.getProbeSequenceData.R
547154594eb81807c33c07336b2a9bdd *R/AffymetrixCdfFile.getSubsetOfCellIndices.R
08250b829935ffad47b3c64b703b72eb *R/AffymetrixCdfFile.getSubsetOfUnits.R
f081cbe8790f1a19d1f5c451ed8321aa *R/AffymetrixCdfFile.getUnitGroupCellMap.R
4d46b4000fc1b16213d98cbe517cbf38 *R/AffymetrixCdfFile.getUnitGroupNamesFromUgcMap.R
9201ed8d4b4aeaba1de596f0b732d7fb *R/AffymetrixCdfFile.groupUnitsByDimension.R
2430fab52d3546bb3d77ed7902dd9508 *R/AffymetrixCdfFile.readDataFrame.R
adaa8b49c169f44fd0443bde21b73cc1 *R/AffymetrixCdfFile.writeCdfByExcludingCells.R
c8b22625a3c8d51be5de9c2ba032a928 *R/AffymetrixCelFile.BG.R
9be612bd762d9fdc936c14fb92d9faec *R/AffymetrixCelFile.PLOT.R
61ca4eebabf8c920fb5be651e6cb6c45 *R/AffymetrixCelFile.R
493a56b1077b67934f6f2858a4472bfa *R/AffymetrixCelFile.allocateFromCdf.R
81897e0bd94cc991028364c0c2139883 *R/AffymetrixCelFile.createFrom.R
6a168dd21663df1b48301d11e15454f3 *R/AffymetrixCelFile.extractMatrix.R
46d0e82ad944fa43f001da59191f1535 *R/AffymetrixCelFile.fitQuantileNormFcn.R
7b48de212e456e4c415d999fde18f641 *R/AffymetrixCelFile.normalizeAffine.R
5906674cfd5f93f4fc7b9895502c7ae3 *R/AffymetrixCelFile.normalizeQuantile.R
f0c0614fc4a8e178c883fa5d98ba8641 *R/AffymetrixCelSet.BG.R
092c3ba17cbb345cd0947862763f6f85 *R/AffymetrixCelSet.NORM.R
c555935789b6018787acc40156a8f97a *R/AffymetrixCelSet.PLOT.R
abde80a1e5d5ffd9b839f69c92c4c9eb *R/AffymetrixCelSet.R
9db4d97c23913c27c7b6ce5a202779b2 *R/AffymetrixCelSet.convertToUnique.R
fb8a7812df7b0c95197fe8f8eac70538 *R/AffymetrixCelSet.extractAffyBatch.R
a5676a64f7fb7ac03ba4606983e04a89 *R/AffymetrixCelSet.extractMatrix.R
4a3f890b66fbe3e9bdfc19fd6aa77ba6 *R/AffymetrixCelSet.extractSnpFeatureSet.R
924cdb008f7991a3ccab23f36fabd212 *R/AffymetrixCelSet.getAverageFile.R
c10f0ea761cfd2caf4b7b5472a7f5bbe *R/AffymetrixCelSet.importFromDChip.R
1c8dec2c9ad5de8dd01052968d8e1807 *R/AffymetrixCelSet.justSNPRMA.R
9fc85375078f7807c75f2590074e7878 *R/AffymetrixCelSet.writeSgr.R
470ffdf56549b6bfa90783bd20c39053 *R/AffymetrixCelSetReporter.R
062f51ec0c233a97bf35257184021569 *R/AffymetrixCelSetTuple.R
ce325fec86a3b231e9c20e0ae3a8d74c *R/AffymetrixCnChpFile.R
73aef415ea70d874049441c450b1964a *R/AffymetrixCnChpSet.R
966a1938a4de0179d29f196930eed4c8 *R/AffymetrixCnChpSet.extras.R
c57a682c6e6757f73612274ec82012e2 *R/AffymetrixCsvFile.R
4c6dfca4bfe620badc63ca353803a708 *R/AffymetrixCsvGenomeInformation.R
5dabb3205e258296f7a12cd4a56ee9e7 *R/AffymetrixFile.R
72dc9b8cd731f6644d288c9aef703267 *R/AffymetrixFileSet.R
dc23c4313d3428faa576597ff0ec7d90 *R/AffymetrixFileSet.getIdentifier.R
0ad98804c68ab7a42314ec725d039a13 *R/AffymetrixFileSetReporter.R
a23b57a6579e0bbff18077b6dd08a442 *R/AffymetrixNetAffxCsvFile.R
45d3696f11fd7358b244f4d5a707548c *R/AffymetrixNetAffxCsvFile.XTRS.R
98ba3bb15b537757a8835a54abaff210 *R/AffymetrixPgfFile.R
8b384a51cc546ccc336bd532c1a631db *R/AffymetrixPlatform.R
6d1d3a802e40d723701db7b18cd4db85 *R/AffymetrixProbeTabFile.R
75b1cdf2650fd45f366fd348c49f0504 *R/AffymetrixTabularFile.R
477a28ce176387fcdb3286a97b0c5417 *R/AffymetrixTsvFile.R
8816100b52a2edc7e46fd0f6a6390fe3 *R/AlleleSummation.R
fe86040904b3894209d5e62deb36464e *R/AllelicCrosstalkCalibration.PLOT.R
46685bd7441976c2d6977b580a0546b1 *R/AllelicCrosstalkCalibration.R
2e0eabbaeb2213477c33e3af8c77b13f *R/AllelicCrosstalkCalibration.getSetsOfProbes.R
de1bb850b37d0f2d0c578336222a49d0 *R/AromaCellCpgFile.AFFX.R
9c4a4794511dea54104b5cbb2ce11847 *R/AromaCellMatchScoreFile.AFFX.R
a94eb7cf97f7e218edb9107918dd2a55 *R/AromaCellMatchScoreFile.R
439f53d95e201b5577069dcf8aca0618 *R/AromaCellMatchScoreFile.importFromBpmap.R
bcd44b82ac924324df0666505a82e6ef *R/AromaCellPositionFile.AFFX.R
ef3758c8c143b8fd4845a4c0ad83afe6 *R/AromaCellSequenceFile.AFFX.R
a6e1b8415553275b72e5c1561061a5ff *R/AromaCellSequenceFile.importFromBpmap.R
7403b534d39fde5465891bca8b716f27 *R/AromaChipTypeAnnotationFile.R
52fd1a874453fa360849c4287d644608 *R/AromaPipeline.R
722f0d36deaf5d8703a4527109b41b9c *R/AromaUfcFile.R
054244b088a13737964be507b9b0f92d *R/AromaUflFile.AFFX.R
339cddb93468710a434918b00c3bed6f *R/AromaUgpFile.AFFX.R
eb3786aeb05c59dd3e72c560df6b596c *R/AromaUnitGcContentFile.AFFX.R
22273e48f09520b1d50972fe8a083a24 *R/AromaUnitGcContentFile.R
4b6bef7bfdc8e508d67a006ca2ba027f *R/AromaUnitTabularBinaryFile.AFFX.PLOT.R
92ee7e1b10cbeb06ba273dd918d56ba5 *R/AromaUnitTabularBinaryFile.AFFX.R
0b0c116f37fee2af115e55e3f65bc777 *R/ArrayExplorer.R
b058614ea68810d17accc7bb5fea6ad5 *R/AvgCnPlm.R
19a202165a4b7fb52884e9f21699b128 *R/AvgPlm.R
f5ea71ef99772265fb32472a1832ecbd *R/AvgSnpPlm.R
1c047d5490c28989aa32732ebd1d02ba *R/BackgroundCorrection.R
c9dfc2811bdb4fa30af970fe2f854e00 *R/BaseCountNormalization.R
8e8fa4b9277c253f8f3db12c67a09623 *R/BasePositionNormalization.R
5030059b3cf74acfe09cb7dc6c4f5224 *R/BasePositionNormalization.getFit.R
2296cbd908836e06edd8a025d7c23bba *R/ChipEffectFile.R
0a635344f94e268f255e8d31d3dfa9ed *R/ChipEffectFile.TOFULL.R
99e7eca31b5377215a885b6f4e841f53 *R/ChipEffectFile.extractTheta.R
52a59f857ff71b03f68ce0590cdf0ca1 *R/ChipEffectFile.fromDataFile.R
22b19b734f1382a2175c59c194f6efff *R/ChipEffectFile.getUnitGroupCellMatrixMap.R
232c7bbf3416461eba52692f45dd8205 *R/ChipEffectFile.xam.R
2be0b6a08bca9c0c738f7c3d46328398 *R/ChipEffectGroupMerge.R
da43f48a98041ea4a58346349b74296f *R/ChipEffectNnn.extractChromosomalDataFrame.R
9315e41742e13ec8afcf5e13bdf1d18d *R/ChipEffectSet.PLOT.R
aa32c56a82fe5f5585e8d1656a45dfc9 *R/ChipEffectSet.R
8e79f39c28e9f0c313c6cc2b2203eb91 *R/ChipEffectSet.STATS.R
89cbb043290c39ccd9c2230d2d35f40b *R/ChipEffectSet.TOFULL.R
f5ee4cbf3b9a4529e6d9b9c9e4ad65cf *R/ChipEffectSet.calculateBaseline.R
4118d1ad8b68cbbf23fd42a6b238a724 *R/ChipEffectSet.extractExpressionSet.R
e15686cd7ce0616a77cbaa424c909392 *R/ChipEffectSet.extractTheta.R
4c7660a7fdf33e644b212c0d795f986e *R/ChipEffectSet.getBaseline.R
f5f59520ce5e07711b1a3922f824ba5d *R/ChipEffectSet.xam.R
ff0d0e537a7d6d8df07bb5fba6455a25 *R/ChipEffectSetTuple.R
d5c4af0b01fcd308662743562b979a9d *R/ChipEffectTransform.R
0c04c9abc4cf1f27ae9000ea12465579 *R/ChromosomalModel.AFFX.R
bc33d80b9a717b8b5ce4d1e9a74f977a *R/ChromosomalModel.getPositionChipTypeUnit.R
354b0a68dcbc92c5c990b121ccdd2fea *R/ChromosomalModel.getXTheta.R
6985e0f35ac974a5d25f47611baec4ca *R/CnChipEffectFile.R
07ca640bd6776f81d23af039f76d35ea *R/CnChipEffectFile.exportAromaSignalBinaryFileList.R
35036efbc821531b10c49257ec9e11a6 *R/CnChipEffectSet.R
253325ca4f6b842530d9cdba7ab32ae9 *R/CnChipEffectSet.importFromApt.R
f86739bd82a0af3db2e50a3c639dcc30 *R/CnChipEffectSet.importFromDChip.R
f21a9aa3738c829448772ac0c434beda *R/CnChipEffectSet.writeWig.R
885557e308583eab6b5790f8bfe215a7 *R/CnChipEffectSetTuple.R
e3c175f0c69672365e1eb10fb46032e9 *R/CnPlm.R
9c6891b3493c249557f136db729daf5f *R/CnProbeAffinityFile.R
3e41842b4cecf7e993e6d2ba83a0eeca *R/CnagCfhFile.R
db9e38e38673e1fe8569bd4311c59d30 *R/CnagCfhSet.R
c693ca22f88137977c0d77c40db4a0ee *R/CopyNumberChromosomalModel.AFFX.R
aac36ecd870b2368e1c2116407745d25 *R/CopyNumberChromosomalModel.applyCCF.R
5ae9f06aa62bbb47fba967670e6b8588 *R/CopyNumberSegmentationModel.migrateTool.R
1231d59e7d8402287c541943eb10b3b7 *R/CrlmmModel.EXT.R
dc4f8dc02f7ac5fe71d6f6c2605f01b9 *R/CrlmmModel.R
802087b3926ced376ce62bd7fc89c231 *R/CrlmmParametersFile.R
f1ad60458bdc32697cb8b1a8760e64d5 *R/CrlmmParametersSet.R
e2c55e38c93066a58e827c67c2e7f4a9 *R/DChipCdfBinFile.R
a2bd9332769c3d60914e966bf2142f3b *R/DChipCdfBinFile.mapToUnitNamesFile.R
c35dabae1667256b629e0354820c729c *R/DChipDcpFile.R
cb0dae4d64c07e0b12eacf60d713ccdc *R/DChipDcpSet.R
4cda610497f184e2659c54db204ca27b *R/DChipDcpSet.extras.R
33239f9fa86242e589d59b790186c22b *R/DChipGenomeInformation.R
7a92689f9b4c18e9c05dbb4f4f51724a *R/DChipQuantileNormalization.R
aed7ff0c2dd1167ab85cbd8a542902c7 *R/DChipSnpInformation.R
99d1db5879010caa5dbf4a83be0d45e3 *R/ExonChipEffectFile.R
50398466031b46873b543e70d25cdabe *R/ExonChipEffectSet.R
da4fdc8fbb50e75592847de36f68bb99 *R/ExonProbeAffinityFile.R
6484129e253d09a54cc83a5548c0c2e6 *R/ExonRmaPlm.R
9ff70abe501370d2edf73e77e895016b *R/ExonRmaPlm.calculateWeights.R
62dcc7824b220583a17bc4fe8d1c3ea9 *R/FirmaFile.R
d00d6309a5f3cf4ed2ef84a740d4d859 *R/FirmaModel.R
c823474795ba82351b38b01f894c631e *R/FirmaSet.R
9b5be74ba63aacdc943708435963047e *R/FragmentEquivalentClassNormalization.R
56f805edb6889aa96050a79088ee2eaa *R/FragmentLengthNormalization.R
db425a685ca4a74ac3ddffde3a84105b *R/GcContentNormalization.R
87de9d5d2bc73be29cb498d44f7fc8e3 *R/GcContentNormalization2.R
b637e479ed25117c161de06bd54c4c0d *R/GcContentNormalization2.plotCovariateEffects.R
737cbca255d92cc84f7fb7023d6dd808 *R/GcRmaBackgroundCorrection.R
1eb4661630365b6330cbe46a493eff8a *R/GenericReporter.R
a5474412e3b7bc5f858ad4eb0038d441 *R/GenomeInformation.AFFX.R
b973f8c79cafbe606a9f56671dfe8bbd *R/GenomeInformation.R
bd3b50493b783372803a9769bd2efcc2 *R/HetLogAddCnPlm.R
95f1ab54f14d4d4cfd38eb30433674d7 *R/HetLogAddPlm.R
27299048b00073e804f390efecec6cf5 *R/HetLogAddSnpPlm.R
b2641354ef4c3e5106f1932557825eb5 *R/LimmaBackgroundCorrection.R
ba4c8f4258ae290baa1d444771970671 *R/LinearModelProbeSequenceNormalization.R
23935534a9a582d4f3b1d91dce8c784d *R/MatNormalization.R
2e8d620144a824569109123f5434112d *R/MatSmoothing.R
8c2ced2ea3d4a4bd781cd6bd48e46d89 *R/MbeiCnPlm.R
8ed8945dbc4eaf283ae3ed2a9c802950 *R/MbeiPlm.R
4b0122c449008a61626dc5acccd6865f *R/MbeiSnpPlm.R
765cccbe4024c62fc552cdd6bde11475 *R/Model.R
df8f199f49043a5b69c190a15787e374 *R/MultiArrayUnitModel.R
4c7e5525d5905402e75fedd944ab1936 *R/NormExpBackgroundCorrection.R
720d690c793b78acff581ebc53d3356f *R/OpticalBackgroundCorrection.R
9388086af14d2145806a908149b6fa41 *R/Package.XTRA.R
92433fa654a9c71690413b991fb73f92 *R/ParameterCelFile.R
09c8392e04efef1142d31f84cc8b98a2 *R/ParameterCelFile.extractNnn.R
7328918923b6dc916dd3ac99cd4bcbc1 *R/ParameterCelSet.R
87132cd54cf4534d6357bf13b3a4d5f7 *R/ProbeAffinityFile.R
6e291e1fe3de2ad1a22629fef55d1861 *R/ProbeLevelModel.R
aeeedd49e526de080cc29876138d70e2 *R/ProbeLevelModel.calculateResiduals.R
851f93605d9e1f67d013d5eee55c0d32 *R/ProbeLevelModel.calculateWeights.R
dadbef7b469bacdb0b35f300718bc42a *R/ProbeLevelModel.fit.R
ce4912ba1ca82b23bade0b0df0c83797 *R/ProbeLevelTransform.R
f4795c34e8699df9e5571e4571052b2e *R/ProbeLevelTransform3.R
ee0e13313622d1960c2e913c57dcde37 *R/QualityAssessmentFile.R
d1ac961fd67b75a7666eaf0a167ece74 *R/QualityAssessmentModel.R
7057d70799c296df1758c1b0710b6b94 *R/QualityAssessmentSet.R
27531e227d9fbb70de7410438c49b572 *R/QuantileNormalization.R
0b46865a2c68399caf944c9f45a6bfe7 *R/QuantileNormalization.xtra.R
72dad84f73dfef0dee1d08b113da0094 *R/ReseqCrosstalkCalibration.R
d033dfa67c57e2b6b44733de34d4e44f *R/ResidualFile.R
cb213e4b027c2885c00d6a9f2fae67fd *R/ResidualSet.R
da33b2d3f6f1e54d0a14930dfcc69884 *R/RmaBackgroundCorrection.R
2bbeec8010f48af5d731a2d5b63e2fad *R/RmaCnPlm.R
84df34d873ad092228eddecd55f81a86 *R/RmaPlm.R
18ad8e9040909daba569ca1ea6e42c9c *R/RmaSnpPlm.R
1e9381a32f482bd3bb8e082718a36b81 *R/ScaleNormalization.R
95656e7aa356cf63b3c4f6d11ac6e29f *R/ScaleNormalization3.R
e102ca5dda9b45af1dd6673c4508a62b *R/SingleArrayUnitModel.R
30590d54bfa936b60934fd286b055830 *R/SingleArrayUnitModel.fit.R
2c94a625adb8374bd2569790beac9cfa *R/SmoothMultiarrayModel.R
3a2db21579f71894cd27795df199d332 *R/SmoothMultiarrayModel.fit.R
c66369acf17852d9bef67f740533e71b *R/SmoothRmaModel.R
628a4f8020633879459c5d3fb981f08c *R/SmoothSaModel.R
ce0975747462bd5e01f033f84f90b6a1 *R/SnpChipEffectFile.R
d79b77c846102c8afe3756bdb81c2409 *R/SnpChipEffectFile.exportTotalAndFracB.R
314602421853ba79caad94009f66cdee *R/SnpChipEffectFile.extractTotalAndFracB.R
4c11ef89b0bf2b79a85c7d7e0d837f6e *R/SnpChipEffectGroupMerge.R
093de1a780186f6a344ef3c9b6000a5d *R/SnpChipEffectNnn.extractCNT.R
79080f3d484f7b66ce1152eae258dab2 *R/SnpChipEffectNnn.writeCNT.R
5efa6d3aca42e340741a32ee74894b78 *R/SnpChipEffectSet.R
125f79fc83053daf2392480b56080594 *R/SnpChipEffectSet.exportTotalAndFracB.R
045d0c2f2ed1e32b60fff6ee93f5903c *R/SnpChipEffectSet.extractAlleleSet.R
2e42be2d95c4924e00a93464dc6c6dc6 *R/SnpChipEffectSet.extractSnpCnvQSet.R
28fbc6e784aeff384f3192e67f7b1007 *R/SnpChipEffectSet.extractSnpQSet.R
185fb11f2116b1fbfa04c93394bde1c5 *R/SnpChipEffectSet.extractTotalAndFreqB.R
e41da8d1cac0535636736be4821751b6 *R/SnpCnvQSet.extractTheta.R
1795772de3a5e1ec995ad206e4b47768 *R/SnpInformation.R
75540fe3f9b61d8964a027983af3c69e *R/SnpPlm.R
864fd2d07858094505eb06e5b3581a60 *R/SnpProbeAffinityFile.R
bf5f30204865b2ddd14564a9efb4ed49 *R/SnpQSet.extractTheta.R
9434bb7cb2ce46178f3b493a2259f7f0 *R/SpatialReporter.R
9467d8890ac3a3fdf8af9b8d7b056dde *R/SpatialRowColumnNormalization.R
7e37628eac57c7efa60dcd2537b37aa3 *R/Transform.R
246136f626a53e95820e46ca11c4db38 *R/TransformReport.R
34d7c6555280575b4db9dd8bc8b7f4e7 *R/UflSnpInformation.R
c8a7e38b1a4afaa9435b902ef161b0d8 *R/UgpGenomeInformation.R
655e80f7dd1c14261bb1253da2867439 *R/UnitModel.R
9836a5a23982007084698cc2811df8c3 *R/UnitModel.fitCnProbes.R
8a3673cb1ea4941833e67be775f29732 *R/UnitTypeScaleNormalization.R
bcd4b46995d7f62f286e792c649256a2 *R/WeightsFile.R
0dbed5b215f73fd94335c5d0556cf7ef *R/WeightsSet.R
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cb749d542ae89db734d653649b2b5028 *man/verify.GenomeInformation.Rd
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da0d8cc43ff7811c0300f36a05acf264 *man/writeImage.AffymetrixCelFile.Rd
