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)
•
written
by
mahejabeen.nidhi •
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
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
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.
Are you running GSEA as the JAVA version on Windows? It would be better to create the file as plain text outside Excel.
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!
Could be some end-line formatting issue that is passed on from Mac Excel - not sure.
Log in to answer this question.
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
there is same problem to me how can i fix it....