help
32 views
Skip to first unread message
Fercho Fercho
May 2, 2023, 5:26:03 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
Castanza, Anthony
May 2, 2023, 7:03:10 PM5/2/23
to gsea...@googlegroups.com
Hi Fercho,
There are a couple issues here, first, GSEA expects data for all genes that would be expected to be expressed in a whole-transcriptome study. 221 features (what is present in your dataset) is not sufficient for GSEA. You should not do things like filter for just significantly differentially expressed genes. This is the first “WARNING” in your log.
Secondly, the CLS format is incorrect. I would encourage you to review the CLS format specification here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29
You’ll also want to ensure that your dataset is formatted in accordance with the GCT file specification also described in the Data_formats documentation.
If you’re still having issues after attempting to correct these errors, please let me know
-Anthony
Anthony S. Castanza, PhD
Department of Medicine
University of California, San Diego
--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/83be0e13-cfb7-4013-902e-10515f764a2bn%40googlegroups.com.
Reply all
Reply to author
Forward
0 new messages