parsing error: expecting 2 columns reading 3 columns

[Sofia Fertuzinhos]

Dear GSEA-help,

I am trying to upload my categorical phenotype cls file (see attached) and I am getting this error:

<Error Details>

---- Full Error Message ----
There were errors: ERROR(S) #:1
Parsing trouble
edu.mit.broad.genome.parsers.Par ...

---- Stack Trace ----
# of exceptions: 1
------Bad format - expect ncols: 2 but found: 3 on line: ?�9L�ҙ �sbgٮ|�l!�� USh9i�b�r:"y_dl��D�� �|-N��R"4 �2�G�%�� Z�4�˝y�7 ë��ɂ� �� �� PK !�>���� xl/_rels/workbook.xml.rels � (� �RMK�0 � ��0w�v �t/"�U� ɴ)�&!3~�� *�]X�K/ o�y���v�5 � ��+�� z l�; o��� b� �G ���� �s �>��,� 8��(% ���"D��҆4j�0u2js� �MY�˴���S쭂��� �)f���C�� ��y �� I<------
edu.mit.broad.genome.parsers.ParserException: Bad format - expect ncols: 2 but found: 3 on line: ?�9L�ҙ �sbgٮ|�l!�� USh9i�b�r:"y_dl��D�� �|-N��R"4 �2�G�%�� Z�4�˝y�7 ë��ɂ� �� �� PK !�>���� xl/_rels/workbook.xml.rels � (� �RMK�0 � ��0w�v �t/"�U� ɴ)�&!3~�� *�]X�K/ o�y���v�5 � ��+�� z l�; o��� b� �G ���� �s �>��,� 8��(% ���"D��҆4j�0u2js� �MY�˴���S쭂��� �)f���C�� ��y �� I<
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.StringDataframeParser._parse(StringDataframeParser.java:164)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.StringDataframeParser.parseSdf(StringDataframeParser.java:144)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser._parse_new_style(ClsParser.java:272)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ClsParser.parse(ClsParser.java:227)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory._readTemplates(ParserFactory.java:341)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readTemplate(ParserFactory.java:292)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:767)
at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:737)
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)

Could you please tell me what am I doing wrong?

Thank you,

Sofia.

[Anthony Castanza]

Hi Sofia,

What it looks like happened here is that you saved the file as an excel format such as xls or xlsx, then renamed it to CLS and tried to load it into GSEA, however GSEA can't the data structure of the proprietary microsoft formats, so instead you first have to save the file as Tab Delimited Text (.txt) (or something like that) from the save as menu, and only then can you change the file extension to .cls.

Let me know if you still have issues after trying this step

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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