Error while reading the gct file

[GenePattern Help Forum]

Dear GenePattern-Team,

 

today, I want to check my gene expression data set according to your recipe “Identify an up- or down-regulated pathway from expression data”. Unfortunately, I get an error at step 4:

 

org.genepattern.io.ParseException: Data at line number 4 and column 0 is not a number.

        at org.genepattern.io.expr.gct.GctParser.readData(GctParser.java:117)

        at org.genepattern.io.expr.gct.GctParser.parse(GctParser.java:77)

        at org.genepattern.io.expr.ReaderUtil.read(ReaderUtil.java:37)

        at org.genepattern.io.expr.gct.GctReader.read(GctReader.java:42)

        at org.genepattern.module.AnalysisUtil.readExpressionData(AnalysisUtil.java:156)

        at org.genepattern.module.AnalysisUtil.readExpressionData(AnalysisUtil.java:177)

        at edu.mit.broad.modules.marker.CreateMarkersFileModule.main(CreateMarkersFileModule.java:174)

An error occured while reading the file Diff.gct.txt.

Cause: Data at line number 4 and column 0 is not a number.

 

Moreover, in step 3 I don´t get a “Score”. But if I compare my gct file with the example, I can´t find my fault.

 

I´m sorry for all the questions and I would be glad if you can help me.

[Barbara Hill]

Hello

I have run through this recipe in GenomeSpace and did not have any trouble with the example data indicated.

I see that you have used your own data - Diff.gct.txt. 

The first issue is that your file ends in txt. It should end in gct.

Then, be sure it matches the correct format of a GCT file - see here.

Please let us know if you need any further assistance.

Best

-Barbara