problema
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Fercho Fercho
May 2, 2023, 5:05:46 PM5/2/23
to gsea-help
Hello, I hope you can help me. I am having the following problem and I have loaded my gct and cls files but when I run the program I get the following error and I have already tried the chip platforms that can be selected and the error continues:
ID A65_C1.sst-rma-combined-dabg.chp l A65_T1.sst-rma-combined-dabg.chp Signal
TC0100006494.hg.1 7.63 4.37
< Process output will appear below >
Done initing things while splashing
[1683059409397] [INFORMACIÓN] Begun importing: Dataset from: gsea con ID.gct
[1683059409506] [WARNING] Loaded dataset with 221 features. This may be too few for GSEA, which expects data for all expressed genes for a proper analysis.
[1683059409522] [INFO] Loaded file: C:\Users\you\Desktop\gsea con ID.gct
[1683059409522] [INFO] <html>Loading ... 1 files<br><br>gsea con ID.gct
<br>Files loaded successfully: 1 / 1<br>There were NO errors<br><br><b>There were warnings. See the [+] console log for details.</b></html>
[1683059445869] [INFO] Begun importing: Template from: gsea CON id CLS.cls
[1683059445885] [SEVERE] There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IllegalArgumentException: Mismatched numbers between unique item id's: 6 [CONTROL1, CONTROL2, CONTROL3, TRATAMIENTO1, TRATAMIENTO2, TRATAMIENTO3] and number of Template.Class's: 2
CONTROL TRATAMIENTO
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.runChecksInit(TemplateImpl.java:326)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.assignItems2ClassInOrder(TemplateImpl.java:372)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate_ordered_assign(TemplateFactory.java:211)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate(TemplateFactory.java:104)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:249)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:225)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:340)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:291)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:765)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
[1683059577729] [INFO] Begun importing: Template from: gsea CON id CLS.cls
[1683059577729] [INFO] Loaded file: C:\Users\you\Desktop\gsea CON id CLS.cls
[1683059577729] [INFO] <html>Loading ... 1 files<br><br>gsea CON id CLS.cls
<br>Files loaded successfully: 1 / 1<br>There were NO errors</html>
>> {zip_report=false, num=100, scoring_scheme=weighted, norm=meandiv, out=C:\Users\yuss\gsea_home\output\may02, mode=Max_probe, include_only_symbols=true, set_max=500, gmx=ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt, plot_top_x=20, nperm=1000, order=descending, rnd_seed=timestamp, rpt_label=my_analysis, set_min=15, res=C:\Users\you\Desktop\gsea con ID.gct, chip=ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip, create_svgs=false, cls=C:\Users\you\Desktop\gsea CON id CLS.cls#TRATAMIENTO_versus_CONTROL, sort=real, create_gcts=false, save_rnd_lists=false, median=false, metric=Signal2Noise, make_sets=true, rnd_type=no_balance, gui=false, permute=gene_set, collapse=Collapse}
# of elements = 1
C:\Users\you\Desktop\gsea CON id CLS.cls#TRATAMIENTO_versus_CONTROL
to parse>ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt< got: [ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt]
[1683059631699] [INFO] File download started. Retrieving h.all.v2023.1.Hs.symbols.gmt from remote server...
[1683059632673] [INFO] Download complete
[1683059632909] [INFO] Begun importing: GeneSetMatrix from: ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt
[1683059633806] [INFO] File download started. Retrieving Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip from remote server...
[1683059644842] [INFO] Download complete
[1683059645089] [INFO] Begun importing: Chip from: ftp://ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip
[1683059645189] [INFO] Parsed from dotchip : 41251
[1683059645204] [INFO] Creating collapsed dataset gsea con ID_collapsed_to_symbols, chosen mode 0
[1683059645204] [WARNING] Collapsed dataset results in 0 features. This may be too few for GSEA, which expects data for all expressed genes for a proper analysis.
[1683059645204] [INFO] Collapsing dataset was done. Original: 221x6 (ann: 221,6,chip na) collapsed: 0x6 (ann: 0,6,ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip)
[1683059645219] [SEVERE] Tool exec error
xtools.api.param.BadParamException: The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.getDataset(Gsea.java:109)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:164)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)
[1683059645235] [INFO] Renaming rpt dir on error to: C:\Users\you\gsea_home\output\may02\error_my_analysis.Gsea.1683059630725
Done initing things while splashing
[1683059409397] [INFORMACIÓN] Begun importing: Dataset from: gsea con ID.gct
[1683059409506] [WARNING] Loaded dataset with 221 features. This may be too few for GSEA, which expects data for all expressed genes for a proper analysis.
[1683059409522] [INFO] Loaded file: C:\Users\you\Desktop\gsea con ID.gct
[1683059409522] [INFO] <html>Loading ... 1 files<br><br>gsea con ID.gct
<br>Files loaded successfully: 1 / 1<br>There were NO errors<br><br><b>There were warnings. See the [+] console log for details.</b></html>
[1683059445869] [INFO] Begun importing: Template from: gsea CON id CLS.cls
[1683059445885] [SEVERE] There were errors: ERROR(S) #:1
Parsing trouble
java.lang.IllegalArgumentException: Mismatched numbers between unique item id's: 6 [CONTROL1, CONTROL2, CONTROL3, TRATAMIENTO1, TRATAMIENTO2, TRATAMIENTO3] and number of Template.Class's: 2
CONTROL TRATAMIENTO
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.runChecksInit(TemplateImpl.java:326)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateImpl.assignItems2ClassInOrder(TemplateImpl.java:372)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate_ordered_assign(TemplateFactory.java:211)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.objects.TemplateFactory.createTemplate(TemplateFactory.java:104)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_genecluster_style_categorical(ClsParser.java:249)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:225)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:340)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:291)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:765)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:735)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:53)
at java.desktop/javax.swing.SwingWorker$1.call(Unknown Source)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.desktop/javax.swing.SwingWorker.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
[1683059577729] [INFO] Begun importing: Template from: gsea CON id CLS.cls
[1683059577729] [INFO] Loaded file: C:\Users\you\Desktop\gsea CON id CLS.cls
[1683059577729] [INFO] <html>Loading ... 1 files<br><br>gsea CON id CLS.cls
<br>Files loaded successfully: 1 / 1<br>There were NO errors</html>
>> {zip_report=false, num=100, scoring_scheme=weighted, norm=meandiv, out=C:\Users\yuss\gsea_home\output\may02, mode=Max_probe, include_only_symbols=true, set_max=500, gmx=ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt, plot_top_x=20, nperm=1000, order=descending, rnd_seed=timestamp, rpt_label=my_analysis, set_min=15, res=C:\Users\you\Desktop\gsea con ID.gct, chip=ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip, create_svgs=false, cls=C:\Users\you\Desktop\gsea CON id CLS.cls#TRATAMIENTO_versus_CONTROL, sort=real, create_gcts=false, save_rnd_lists=false, median=false, metric=Signal2Noise, make_sets=true, rnd_type=no_balance, gui=false, permute=gene_set, collapse=Collapse}
# of elements = 1
C:\Users\you\Desktop\gsea CON id CLS.cls#TRATAMIENTO_versus_CONTROL
to parse>ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt< got: [ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt]
[1683059631699] [INFO] File download started. Retrieving h.all.v2023.1.Hs.symbols.gmt from remote server...
[1683059632673] [INFO] Download complete
[1683059632909] [INFO] Begun importing: GeneSetMatrix from: ftp.broadinstitute.org://pub/gsea/msigdb/human/gene_sets/h.all.v2023.1.Hs.symbols.gmt
[1683059633806] [INFO] File download started. Retrieving Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip from remote server...
[1683059644842] [INFO] Download complete
[1683059645089] [INFO] Begun importing: Chip from: ftp://ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip
[1683059645189] [INFO] Parsed from dotchip : 41251
[1683059645204] [INFO] Creating collapsed dataset gsea con ID_collapsed_to_symbols, chosen mode 0
[1683059645204] [WARNING] Collapsed dataset results in 0 features. This may be too few for GSEA, which expects data for all expressed genes for a proper analysis.
[1683059645204] [INFO] Collapsing dataset was done. Original: 221x6 (ann: 221,6,chip na) collapsed: 0x6 (ann: 0,6,ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip)
[1683059645219] [SEVERE] Tool exec error
xtools.api.param.BadParamException: The collapsed dataset was empty when used with chip:ftp.broadinstitute.org://pub/gsea/msigdb/human/annotations/Human_AFFY_HG_U133_MSigDB.v2023.1.Hs.chip
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.getDataset(Gsea.java:109)
at org.gsea_msigdb.gsea/xtools.gsea.Gsea.execute(Gsea.java:164)
at org.gsea_msigdb.gsea/edu.mit.broad.xbench.tui.TaskManager$ToolRunnable.run(TaskManager.java:391)
at java.base/java.lang.Thread.run(Unknown Source)
[1683059645235] [INFO] Renaming rpt dir on error to: C:\Users\you\gsea_home\output\may02\error_my_analysis.Gsea.1683059630725
My data type has the following format and I use fluorescence data:
ID A65_C1.sst-rma-combined-dabg.chp l A65_T1.sst-rma-combined-dabg.chp Signal
TC0100006494.hg.1 7.63 4.37
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