GSEA expression dataset error update

Question

[mahejabeen.nidhi]

I created the expression dataset using the normalised counts from DESeq2. First few rows are as follows

hashtag1.2                          
60668   6                       
NAME    description R848rep1    R848rep2    R848rep3    noRNArep1   noRNArep2   noRNArep3

ENSG00000000005 NA  0   0   0   0   0   0

ENSG00000000419 NA  1.172406374 8.170678509 2.426862007 2.415256486 0   2.107016851

ENSG00000000457 NA  233.3088685 218.7926134 201.4295466 292.2460348 210.5499811 215.9692272

ENSG00000000460 NA  171.1713306 177.0313677 120.7363849 181.1442364 176.174474  148.544688

ENSG00000000938 NA  0   0   0   0   0   0

ENSG00000000971 NA  0   0   0   0   0   0

ENSG00000001036 NA  0   4.539265839 2.426862007 3.622884729 1.074234597 7.374558977

I also created the phenotype label as follows

6 2 1                   
hashtag R848 noRNA                  
R848    R848    R848    noRNA   noRNA   noRNA

Below is the error message. Very grateful for insight.

<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: 8 on line >NAME   description R848rep1    R848rep2    R848rep3    noRNArep1   noRNArep2   noRNArep3<
If this dataset has missing values, use ImputeDataset to fill these in before importing as a Dataset------
edu.mit.broad.genome.parsers.ParserException: Bad format - expect ncols: 2 but found: 8 on line >NAME   description R848rep1    R848rep2    R848rep3    noRNArep1   noRNArep2   noRNArep3<
If this dataset has missing values, use ImputeDataset to fill these in before importing as a Dataset
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser._parseNoDesc(TxtDatasetParser.java:146)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:130)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.TxtDatasetParser.parse(TxtDatasetParser.java:86)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.readDatasetTXT(ParserFactory.java:201)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:748)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserFactory.read(ParserFactory.java:725)
    at org.gsea_msigdb.gsea/edu.mit.broad.genome.parsers.ParserWorker.doInBackground(ParserWorker.java:51)
    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)

[geoski7]

I don't know whether you still have this problem or not, however mine was solved when I removed all the spaces from the name of the file. eg. expression file 1 => expressionfile1

[hs960201]

there is same problem to me how can i fix it....

Answer 1

[hs960201]

i just found the answer of mine , just change extension name manually

ex) smaple.txt -> sample.gct

if you don't solve your problem yet try this method

Answer 2

[Kevin Blighe]

Hi,

The layout should be:

#1.2                            
60668<TAB>6                     
NAME<TAB>description<TAB>R848rep1<TAB>R848rep2<TAB>R848rep3<TAB>noRNArep1<TAB>noRNArep2<TAB>noRNArep3

Obviously, where I have <TAB>, you should have a tab space.

Kevin

[mahejabeen.nidhi]

Thank you, Kevin I created the file on excel and saved it as tab delimited text so I would assume it to be just like your layout. I also did put a # where I wrote hashtag.

[Kevin Blighe]

Are you running GSEA as the JAVA version on Windows? It would be better to create the file as plain text outside Excel.

[mahejabeen.nidhi]

I was just reading about why not to use excel! I am running the GUI of GSEA on my macbook. I will let you know if it works out this time. Thank you so much!

[Kevin Blighe]

Could be some end-line formatting issue that is passed on from Mac Excel - not sure.