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broadinstitute / ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
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Sorry，last problem that the result of local R ssGSEA is #13

Closed Lilab-SYSU closed 4 years ago

Lilab-SYSU commented 4 years ago

This is GenePattern parameter： Input Parameter Display Value Actual Value input gct file GSE107943_RPKM_exprs_unique.gct output file prefix test test gene sets database files gene.sets.database.files.list.txt
gene symbol column Column 1 Name gene set selection ALL ALL sample normalization method none none weighting exponent 0.75 0.75 min gene set size 10 10 combine mode combine.add combine.add

This is Local R ssGSEA parameter：

2019-10-18 23:23:28

input gct: GSE107943_RPKM_exprs_unique.gct gene.set.database: db/msigdb/test.gmt sample.norm.type: none weight: 0.75 statistic: area.under.RES output.score.type ES nperm: 1000 global.fdr: FALSE min.overlap: 10 correl.type: z.score export.signat.gct: TRUE run.parallel: TRUE

but i can't get same results，so i don't know which one is right，I am sorry to trouble you!

Lilab-SYSU commented 4 years ago

This local R ssGSEA results:

1.3

1 57 117 0 id Signature.set.description Signature.set.size Signature.set.overlap.percent.s_081124004_001_RPKM Signature.set.overlap.percent.s_081124004_006_RPKM Signature.set.overlap.percent.s_081203007_001_RPKM Signature.set.overlap.percent.s_081212005_002_RPKM Signature.set.overlap.percent.s_081212005_006_RPKM Signature.set.overlap.percent.s_090715009_001_RPKM Signature.set.overlap.percent.s_090715009_009_RPKM Signature.set.overlap.percent.s_091014006_001_RPKM Signature.set.overlap.percent.s_091014006_006_RPKM Signature.set.overlap.percent.s_091216005_001_RPKM Signature.set.overlap.percent.s_091216005_011_RPKM Signature.set.overlap.percent.s_100202007_001_RPKM Signature.set.overlap.percent.s_100202007_010_RPKM Signature.set.overlap.percent.s_100315003_001_RPKM Signature.set.overlap.percent.s_100315003_011_RPKM Signature.set.overlap.percent.s_100428011_001_RPKM Signature.set.overlap.percent.s_100428011_011_RPKM Signature.set.overlap.percent.s_100712007_001_RPKM Signature.set.overlap.percent.s_100712007_011_RPKM Signature.set.overlap.percent.s_110308013_007_RPKM Signature.set.overlap.percent.s_111227013_001_RPKM Signature.set.overlap.percent.s_111227013_011_RPKM Signature.set.overlap.percent.s_120723019_003_RPKM Signature.set.overlap.percent.s_120723019_011_RPKM Signature.set.overlap.percent.s_120725012_001_RPKM Signature.set.overlap.percent.s_120725012_009_RPKM Signature.set.overlap.percent.s_120813017_001_RPKM Signature.set.overlap.percent.s_120813017_008_RPKM Signature.set.overlap.percent.s_120926009_001_RPKM Signature.set.overlap.percent.s_120926009_008_RPKM Signature.set.overlap.percent.s_121119027_001_RPKM Signature.set.overlap.percent.s_121119027_005_RPKM Signature.set.overlap.percent.s_130128020_001_RPKM Signature.set.overlap.percent.s_130128020_007_RPKM Signature.set.overlap.percent.s_130625010_001_RPKM Signature.set.overlap.percent.s_130625010_012_RPKM Signature.set.overlap.percent.s_130716009_001_RPKM Signature.set.overlap.percent.s_130717008_001_RPKM Signature.set.overlap.percent.s_131015008_001_RPKM Signature.set.overlap.percent.s_131015008_007_RPKM Signature.set.overlap.percent.s_140317035_002_RPKM Signature.set.overlap.percent.s_140317035_011_RPKM Signature.set.overlap.percent.s_140421025_001_RPKM Signature.set.overlap.percent.s_140421025_011_RPKM Signature.set.overlap.percent.s_140819015_001_RPKM Signature.set.overlap.percent.s_140819015_011_RPKM Signature.set.overlap.percent.s_140827007_001_RPKM Signature.set.overlap.percent.s_140827007_011_RPKM Signature.set.overlap.percent.s_141104018_010_RPKM Signature.set.overlap.percent.s_141104018_020_RPKM Signature.set.overlap.percent.s_150106014_001_RPKM Signature.set.overlap.percent.s_150106014_011_RPKM Signature.set.overlap.percent.s_150306011_001_RPKM Signature.set.overlap.percent.s_150306011_011_RPKM Signature.set.overlap.percent.s_80428002_RPKM Signature.set.overlap.percent.s_80428007_RPKM Signature.set.overlap.percent.s_81203007_007_RPKM Signature.set.overlap.s_081124004_001_RPKM Signature.set.overlap.s_081124004_006_RPKM Signature.set.overlap.s_081203007_001_RPKM Signature.set.overlap.s_081212005_002_RPKM Signature.set.overlap.s_081212005_006_RPKM Signature.set.overlap.s_090715009_001_RPKM Signature.set.overlap.s_090715009_009_RPKM Signature.set.overlap.s_091014006_001_RPKM Signature.set.overlap.s_091014006_006_RPKM Signature.set.overlap.s_091216005_001_RPKM Signature.set.overlap.s_091216005_011_RPKM Signature.set.overlap.s_100202007_001_RPKM Signature.set.overlap.s_100202007_010_RPKM Signature.set.overlap.s_100315003_001_RPKM Signature.set.overlap.s_100315003_011_RPKM Signature.set.overlap.s_100428011_001_RPKM Signature.set.overlap.s_100428011_011_RPKM Signature.set.overlap.s_100712007_001_RPKM Signature.set.overlap.s_100712007_011_RPKM Signature.set.overlap.s_110308013_007_RPKM Signature.set.overlap.s_111227013_001_RPKM Signature.set.overlap.s_111227013_011_RPKM Signature.set.overlap.s_120723019_003_RPKM Signature.set.overlap.s_120723019_011_RPKM Signature.set.overlap.s_120725012_001_RPKM Signature.set.overlap.s_120725012_009_RPKM Signature.set.overlap.s_120813017_001_RPKM Signature.set.overlap.s_120813017_008_RPKM Signature.set.overlap.s_120926009_001_RPKM Signature.set.overlap.s_120926009_008_RPKM Signature.set.overlap.s_121119027_001_RPKM Signature.set.overlap.s_121119027_005_RPKM Signature.set.overlap.s_130128020_001_RPKM Signature.set.overlap.s_130128020_007_RPKM Signature.set.overlap.s_130625010_001_RPKM Signature.set.overlap.s_130625010_012_RPKM Signature.set.overlap.s_130716009_001_RPKM Signature.set.overlap.s_130717008_001_RPKM Signature.set.overlap.s_131015008_001_RPKM Signature.set.overlap.s_131015008_007_RPKM Signature.set.overlap.s_140317035_002_RPKM Signature.set.overlap.s_140317035_011_RPKM Signature.set.overlap.s_140421025_001_RPKM Signature.set.overlap.s_140421025_011_RPKM Signature.set.overlap.s_140819015_001_RPKM Signature.set.overlap.s_140819015_011_RPKM Signature.set.overlap.s_140827007_001_RPKM Signature.set.overlap.s_140827007_011_RPKM Signature.set.overlap.s_141104018_010_RPKM Signature.set.overlap.s_141104018_020_RPKM Signature.set.overlap.s_150106014_001_RPKM Signature.set.overlap.s_150106014_011_RPKM Signature.set.overlap.s_150306011_001_RPKM Signature.set.overlap.s_150306011_011_RPKM Signature.set.overlap.s_80428002_RPKM Signature.set.overlap.s_80428007_RPKM Signature.set.overlap.s_81203007_007_RPKM No.columns.scored s_081124004_001_RPKM s_081124004_006_RPKM s_081203007_001_RPKM s_081212005_002_RPKM s_081212005_006_RPKM s_090715009_001_RPKM s_090715009_009_RPKM s_091014006_001_RPKM s_091014006_006_RPKM s_091216005_001_RPKM s_091216005_011_RPKM s_100202007_001_RPKM s_100202007_010_RPKM s_100315003_001_RPKM s_100315003_011_RPKM s_100428011_001_RPKM s_100428011_011_RPKM s_100712007_001_RPKM s_100712007_011_RPKM s_110308013_007_RPKM s_111227013_001_RPKM s_111227013_011_RPKM s_120723019_003_RPKM s_120723019_011_RPKM s_120725012_001_RPKM s_120725012_009_RPKM s_120813017_001_RPKM s_120813017_008_RPKM s_120926009_001_RPKM s_120926009_008_RPKM s_121119027_001_RPKM s_121119027_005_RPKM s_130128020_001_RPKM s_130128020_007_RPKM s_130625010_001_RPKM s_130625010_012_RPKM s_130716009_001_RPKM s_130717008_001_RPKM s_131015008_001_RPKM s_131015008_007_RPKM s_140317035_002_RPKM s_140317035_011_RPKM s_140421025_001_RPKM s_140421025_011_RPKM s_140819015_001_RPKM s_140819015_011_RPKM s_140827007_001_RPKM s_140827007_011_RPKM s_141104018_010_RPKM s_141104018_020_RPKM s_150106014_001_RPKM s_150106014_011_RPKM s_150306011_001_RPKM s_150306011_011_RPKM s_80428002_RPKM s_80428007_RPKM s_81203007_007_RPKM KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM 159 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 12.6 PKLR|GUK1|AK2|POLR3GL|AK4|ADSS|AMPD2|POLR3C|NME7|PRUNE|PDE4B|NPR1|ADCY10|ADCY3|RRM2|ALLC|NT5C1B|AK5|NT5C1A|AMPD1 GUK1|POLR3GL|ADSS|NME7|AK2|POLR3C|PRUNE|RRM2|ADCY3|AMPD2|AK4|PDE4B|PKLR|NT5C1B|NPR1|AK5|ADCY10|ALLC|AMPD1|NT5C1A PKLR|GUK1|AK4|AK2|POLR3GL|ADSS|POLR3C|NME7|AMPD2|PRUNE|ADCY10|NPR1|PDE4B|RRM2|ADCY3|ALLC|NT5C1B|AMPD1|NT5C1A|AK5 GUK1|PKLR|AK2|POLR3GL|AK4|ADSS|AMPD2|POLR3C|PRUNE|NME7|NPR1|PDE4B|ADCY3|RRM2|ADCY10|ALLC|NT5C1B|AMPD1|NT5C1A|AK5 GUK1|AK4|POLR3GL|PKLR|ADSS|PRUNE|NME7|AK2|POLR3C|AMPD2|RRM2|ADCY3|NPR1|ADCY10|NT5C1B|PDE4B|AMPD1|ALLC|AK5|NT5C1A GUK1|AK2|POLR3GL|PKLR|AK4|ADSS|AMPD2|POLR3C|NME7|PRUNE|NPR1|PDE4B|ADCY10|ADCY3|RRM2|ALLC|NT5C1B|AMPD1|AK5|NT5C1A GUK1|AK2|POLR3GL|NME7|AK4|ADSS|RRM2|POLR3C|PRUNE|AMPD2|ADCY3|PKLR|NPR1|AK5|PDE4B|NT5C1B|ADCY10|AMPD1|NT5C1A|ALLC GUK1|AK2|POLR3GL|AK4|PKLR|ADSS|AMPD2|POLR3C|PRUNE|NME7|NPR1|PDE4B|ADCY3|ADCY10|RRM2|ALLC|NT5C1B|AK5|NT5C1A|AMPD1 GUK1|AK2|POLR3GL|ADSS|RRM2|POLR3C|AK4|NME7|ADCY3|AMPD2|PRUNE|PDE4B|NPR1|NT5C1B|ALLC|AK5|PKLR|ADCY10|NT5C1A|AMPD1 PKLR|AK4|AK2|GUK1|POLR3GL|ADSS|AMPD2|PRUNE|POLR3C|NME7|ADCY10|NPR1|PDE4B|ADCY3|ALLC|NT5C1B|RRM2|NT5C1A|AK5|AMPD1 GUK1|AK2|POLR3GL|NME7|POLR3C|ADSS|PRUNE|AMPD2|RRM2|AK4|NPR1|ADCY3|PDE4B|NT5C1B|PKLR|AMPD1|AK5|ALLC|ADCY10|NT5C1A PKLR|GUK1|POLR3GL|AK2|AK4|ADSS|AMPD2|NME7|PRUNE|POLR3C|PDE4B|ADCY10|NPR1|ADCY3|RRM2|ALLC|NT5C1B|AMPD1|NT5C1A|AK5 GUK1|NME7|AK2|POLR3GL|AK4|ADSS|AMPD2|POLR3C|PRUNE|RRM2|ADCY3|NPR1|PDE4B|NT5C1B|PKLR|ADCY10|AK5|NT5C1A|AMPD1|ALLC PKLR|AK4|POLR3GL|AK2|GUK1|ADSS|AMPD2|POLR3C|PRUNE|NME7|NPR1|PDE4B|ADCY3|ADCY10|RRM2|NT5C1B|AMPD1|ALLC|AK5|NT5C1A GUK1|AK2|POLR3GL|POLR3C|ADSS|PRUNE|NME7|RRM2|AK4|ADCY3|AMPD2|PKLR|PDE4B|NPR1|NT5C1B|ADCY10|NT5C1A|AK5|AMPD1|ALLC PKLR|AK4|GUK1|AK2|POLR3GL|ADSS|PRUNE|AMPD2|POLR3C|NME7|ADCY10|NPR1|PDE4B|RRM2|ADCY3|ALLC|NT5C1B|AK5|NT5C1A|AMPD1 GUK1|NME7|AK2|RRM2|ADSS|POLR3GL|PRUNE|POLR3C|AMPD2|AK4|ADCY3|PKLR|PDE4B|AK5|NPR1|ADCY10|NT5C1B|ALLC|NT5C1A|AMPD1 PKLR|GUK1|AK4|POLR3GL|AK2|ADSS|AMPD2|POLR3C|NME7|PRUNE|NPR1|PDE4B|ADCY3|ADCY10|NT5C1B|RRM2|ALLC|AMPD1|AK5|NT5C1A GUK1|AK2|POLR3GL|POLR3C|RRM2|ADSS|NME7|PRUNE|ADCY3|AMPD2|AK4|PKLR|NPR1|PDE4B|NT5C1B|ADCY10|NT5C1A|AK5|AMPD1|ALLC GUK1|AK2|POLR3GL|NME7|ADSS|POLR3C|PRUNE|ADCY3|AMPD2|RRM2|NPR1|AK4|NT5C1B|ADCY10|PDE4B|ALLC|AK5|PKLR|AMPD1|NT5C1A GUK1|AK4|AK2|POLR3GL|PKLR|NME7|PRUNE|ADSS|AMPD2|POLR3C|NPR1|ADCY10|PDE4B|ADCY3|RRM2|ALLC|NT5C1B|AK5|NT5C1A|AMPD1 GUK1|NME7|AK2|RRM2|AK4|POLR3GL|ADSS|POLR3C|PRUNE|AMPD2|ADCY3|PDE4B|NPR1|PKLR|NT5C1B|ALLC|AMPD1|ADCY10|AK5|NT5C1A GUK1|POLR3GL|AK2|AK4|PKLR|ADSS|POLR3C|AMPD2|NME7|PRUNE|NPR1|ADCY3|PDE4B|ADCY10|RRM2|ALLC|NT5C1B|AK5|AMPD1|NT5C1A GUK1|POLR3GL|NME7|AK2|POLR3C|ADSS|PRUNE|AMPD2|PDE4B|AK4|ADCY3|RRM2|NPR1|NT5C1B|ADCY10|PKLR|AK5|ALLC|NT5C1A|AMPD1 GUK1|PKLR|AK2|POLR3GL|AK4|POLR3C|ADSS|NME7|AMPD2|PRUNE|NPR1|PDE4B|ADCY3|RRM2|ADCY10|NT5C1B|ALLC|AMPD1|AK5|NT5C1A GUK1|NME7|AK2|ADSS|POLR3GL|POLR3C|RRM2|PRUNE|AK4|AMPD2|ADCY3|NPR1|PDE4B|PKLR|AK5|NT5C1B|ALLC|ADCY10|NT5C1A|AMPD1 GUK1|POLR3GL|AK2|AK4|PKLR|ADSS|NME7|AMPD2|POLR3C|PRUNE|NPR1|ADCY3|PDE4B|ADCY10|NT5C1B|ALLC|RRM2|AMPD1|AK5|NT5C1A GUK1|NME7|POLR3GL|AK2|AK4|ADSS|AMPD2|POLR3C|PKLR|ADCY3|PRUNE|RRM2|PDE4B|NPR1|ALLC|AMPD1|ADCY10|NT5C1B|AK5|NT5C1A PKLR|AK4|POLR3GL|GUK1|AK2|ADSS|PRUNE|AMPD2|POLR3C|NME7|NPR1|ADCY10|PDE4B|ADCY3|NT5C1B|ALLC|RRM2|NT5C1A|AK5|AMPD1 POLR3GL|NME7|GUK1|POLR3C|AK2|PRUNE|ADSS|AMPD2|ADCY3|RRM2|NPR1|AK4|NT5C1B|PDE4B|ALLC|PKLR|ADCY10|AK5|AMPD1|NT5C1A GUK1|PKLR|POLR3GL|AK2|AK4|ADSS|AMPD2|PRUNE|NME7|POLR3C|PDE4B|ADCY10|NPR1|ADCY3|ALLC|NT5C1B|RRM2|AK5|AMPD1|NT5C1A GUK1|AK2|RRM2|ADSS|POLR3GL|NME7|POLR3C|PRUNE|AMPD2|AK4|ADCY3|NT5C1B|PKLR|PDE4B|NPR1|ALLC|AK5|AMPD1|ADCY10|NT5C1A PKLR|AK2|AK4|GUK1|POLR3GL|ADSS|POLR3C|NME7|AMPD2|PRUNE|NPR1|PDE4B|ADCY10|NT5C1B|ADCY3|RRM2|ALLC|AMPD1|AK5|NT5C1A POLR3GL|GUK1|AK2|ADSS|NME7|RRM2|PRUNE|POLR3C|AK4|AMPD2|PKLR|ADCY3|NPR1|ADCY10|PDE4B|NT5C1B|AMPD1|ALLC|AK5|NT5C1A GUK1|PKLR|POLR3GL|AK2|AK4|ADSS|AMPD2|NME7|POLR3C|PRUNE|NPR1|PDE4B|ADCY3|ADCY10|NT5C1B|RRM2|ALLC|AMPD1|NT5C1A|AK5 GUK1|AK2|POLR3GL|ADSS|RRM2|POLR3C|AMPD2|PRUNE|NME7|AK4|ADCY3|NPR1|PKLR|PDE4B|NT5C1B|AK5|ADCY10|AMPD1|ALLC|NT5C1A GUK1|AK2|POLR3GL|ADSS|NME7|POLR3C|AMPD2|PRUNE|AK4|ADCY3|PDE4B|RRM2|NPR1|AMPD1|NT5C1B|PKLR|ALLC|AK5|ADCY10|NT5C1A GUK1|NME7|AK2|POLR3GL|ADSS|POLR3C|PRUNE|AMPD2|NPR1|ADCY3|RRM2|PKLR|AK4|NT5C1B|PDE4B|ALLC|ADCY10|AK5|AMPD1|NT5C1A PKLR|GUK1|POLR3GL|AK4|AK2|AMPD2|ADSS|PRUNE|POLR3C|NME7|ADCY10|NPR1|PDE4B|ADCY3|ALLC|NT5C1B|RRM2|AMPD1|NT5C1A|AK5 GUK1|ADSS|AK2|POLR3GL|NME7|POLR3C|PRUNE|PKLR|AK4|AMPD2|NPR1|ADCY3|RRM2|PDE4B|NT5C1B|AK5|AMPD1|ALLC|ADCY10|NT5C1A GUK1|POLR3GL|PKLR|AK2|AK4|AMPD2|PRUNE|POLR3C|NME7|ADSS|NPR1|PDE4B|ADCY3|ADCY10|ALLC|NT5C1B|RRM2|AMPD1|AK5|NT5C1A GUK1|AK2|POLR3GL|RRM2|NME7|ADCY3|ADSS|AK4|PRUNE|POLR3C|AMPD2|NPR1|PKLR|PDE4B|NT5C1B|ALLC|AMPD1|ADCY10|AK5|NT5C1A PKLR|GUK1|AK4|AK2|POLR3GL|AMPD2|NME7|PRUNE|POLR3C|ADSS|NPR1|ADCY10|PDE4B|ADCY3|ALLC|RRM2|NT5C1B|AMPD1|NT5C1A|AK5 GUK1|AK2|AK4|POLR3GL|ADSS|PRUNE|NME7|POLR3C|AMPD2|RRM2|ADCY3|NPR1|NT5C1B|AK5|PKLR|ADCY10|PDE4B|AMPD1|NT5C1A|ALLC GUK1|PKLR|POLR3GL|AK2|AK4|AMPD2|ADSS|NME7|POLR3C|PRUNE|NPR1|ADCY10|PDE4B|ADCY3|NT5C1B|ALLC|RRM2|AK5|NT5C1A|AMPD1 GUK1|POLR3GL|NME7|AK4|AK2|RRM2|ADSS|POLR3C|PRUNE|ADCY3|AMPD2|NPR1|NT5C1B|PDE4B|PKLR|AMPD1|ALLC|ADCY10|AK5|NT5C1A PKLR|AK4|GUK1|AK2|POLR3GL|ADSS|AMPD2|NME7|PRUNE|POLR3C|ADCY10|PDE4B|NPR1|ADCY3|NT5C1B|ALLC|RRM2|AMPD1|NT5C1A|AK5 GUK1|POLR3GL|ADSS|POLR3C|PRUNE|AK2|NME7|RRM2|AK4|AMPD2|ADCY3|PKLR|NPR1|NT5C1B|PDE4B|ALLC|ADCY10|AK5|AMPD1|NT5C1A GUK1|AK2|POLR3GL|PKLR|AK4|ADSS|NME7|POLR3C|AMPD2|NPR1|PRUNE|PDE4B|ADCY3|ADCY10|NT5C1B|ALLC|RRM2|AK5|NT5C1A|AMPD1 GUK1|AK2|AMPD2|POLR3GL|PRUNE|ADSS|RRM2|POLR3C|ADCY3|NME7|PDE4B|NPR1|PKLR|NT5C1B|ADCY10|AK4|ALLC|AMPD1|AK5|NT5C1A AK4|AK2|POLR3GL|PKLR|GUK1|ADSS|AMPD2|PRUNE|NME7|POLR3C|PDE4B|ADCY10|NPR1|RRM2|NT5C1B|ADCY3|ALLC|AK5|NT5C1A|AMPD1 GUK1|NME7|POLR3GL|AK2|PRUNE|PKLR|POLR3C|NPR1|AK4|ADSS|AMPD2|ADCY3|RRM2|ADCY10|PDE4B|ALLC|NT5C1B|AK5|AMPD1|NT5C1A PKLR|GUK1|AK2|POLR3GL|AK4|ADSS|POLR3C|AMPD2|NME7|PRUNE|NPR1|ADCY10|ADCY3|PDE4B|NT5C1B|ALLC|RRM2|AMPD1|NT5C1A|AK5 AK2|NME7|GUK1|POLR3GL|ADSS|POLR3C|AMPD2|PRUNE|ADCY3|AK4|PKLR|RRM2|NPR1|PDE4B|NT5C1B|ADCY10|AK5|NT5C1A|AMPD1|ALLC PKLR|GUK1|POLR3GL|AK2|AK4|AMPD2|ADSS|POLR3C|PRUNE|NPR1|ADCY10|NME7|ADCY3|PDE4B|RRM2|ALLC|NT5C1B|AMPD1|AK5|NT5C1A GUK1|NME7|AK2|RRM2|AK4|POLR3GL|POLR3C|ADSS|AMPD2|ADCY3|PRUNE|PDE4B|NPR1|AK5|NT5C1B|ALLC|PKLR|ADCY10|NT5C1A|AMPD1 GUK1|NME7|AK2|POLR3GL|RRM2|POLR3C|ADSS|AK4|PRUNE|ADCY3|AMPD2|PDE4B|PKLR|NPR1|NT5C1B|ADCY10|AK5|NT5C1A|AMPD1|ALLC 57 1412.1682 1173.469 1381.1962 1317.0821 1250.3527 1487.9278 1107.3972 1360.3829 1259.0307 1319.8146 1359.231 1416.2367 1069.7073 1312.3542 1007.7 1389.7761 1219.7445 1401.5903 1041.29 1327.2171 1321.6525 1301.2688 1453.5613 1080.2981 1399.1139 1282.7243 1372.3031 1408.7756 1229.7386 1165.2618 1373.0312 1229.4214 1463.0609 1297.6972 1350.2391 1327.9156 1360.676 1102.9929 1347.0791 1331.9284 1482.3412 1319.8684 1286.2829 1241.2156 1279.0035 1059.0281 1355.7894 1245.7092 1335.0677 1173.0419 1423.307 1281.3805 1273.1157 1075.8981 1382.3635 1400.5717 1322.7808

This is GenePattern Result:

1.2

1 57 Name Description s_081124004_001_RPKM s_081124004_006_RPKM s_081203007_001_RPKM s_081212005_002_RPKM s_081212005_006_RPKM s_090715009_001_RPKM s_090715009_009_RPKM s_091014006_001_RPKM s_091014006_006_RPKM s_091216005_001_RPKM s_091216005_011_RPKM s_100202007_001_RPKM s_100202007_010_RPKM s_100315003_001_RPKM s_100315003_011_RPKM s_100428011_001_RPKM s_100428011_011_RPKM s_100712007_001_RPKM s_100712007_011_RPKM s_110308013_007_RPKM s_111227013_001_RPKM s_111227013_011_RPKM s_120723019_003_RPKM s_120723019_011_RPKM s_120725012_001_RPKM s_120725012_009_RPKM s_120813017_001_RPKM s_120813017_008_RPKM s_120926009_001_RPKM s_120926009_008_RPKM s_121119027_001_RPKM s_121119027_005_RPKM s_130128020_001_RPKM s_130128020_007_RPKM s_130625010_001_RPKM s_130625010_012_RPKM s_130716009_001_RPKM s_130717008_001_RPKM s_131015008_001_RPKM s_131015008_007_RPKM s_140317035_002_RPKM s_140317035_011_RPKM s_140421025_001_RPKM s_140421025_011_RPKM s_140819015_001_RPKM s_140819015_011_RPKM s_140827007_001_RPKM s_140827007_011_RPKM s_141104018_010_RPKM s_141104018_020_RPKM s_150106014_001_RPKM s_150106014_011_RPKM s_150306011_001_RPKM s_150306011_011_RPKM s_80428002_RPKM s_80428007_RPKM s_81203007_007_RPKM KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM 16299.4608658231 19989.5447149386 16339.7566004693 17209.0919003687 20797.6202783133 16821.3314066488 20881.0610342507 16906.8406265591 22502.771299098 16685.1260062009 19957.6955401702 16505.2710717436 20749.3054375068 16611.9938968404 20874.5316867624 15854.8784827201 19476.4821329728 16736.1447994353 20456.456855984 21417.2191868461 17161.2630205658 20215.7079023853 17281.7463412716 20043.7786905117 16813.2751870268 20567.0352544714 16426.432363331 19509.9844072859 16302.7094791352 20774.590529039 15742.9661925763 20604.8223888136 15833.9285730807 19921.6713511367 16172.6869489219 20638.4405044427 19839.3019801299 20239.4674566752 16714.786633289 19120.8363405507 16977.267669876 20524.9636143802 16695.8150829601 21461.8323617545 16336.0452826167 20650.6418440459 16123.007968953 20500.8578954125 16576.3381263648 22379.7382283261 15707.1991622233 20229.8383240883 16915.381532571 20669.4981831811 17151.6400477726 20985.7553607026 22432.6215428183

The same gene set ,but the score is different .For example ,last sample scores: local R ssGSEA:1322.7808 ; GenePattern 22432.6215428183

karstenkrug commented 4 years ago

https://github.com/broadinstitute/ssGSEA2.0/issues/10#issuecomment-543212983