Continuous error of file format when uploading .rnk file for GSEA

[Varun Venkatesh]

Hi there

I can't seem to figure out the issue with uploading a .rnk file to webgestalt. So far my workflow is as follows.

1. Firstly I established a piece of R code I found online to generate a list of gene names and ranks as attached and it gives me the following output example

      Name    metric

1    ENSRNOG00000026310 -1.792287

2    ENSRNOG00000029912  4.090444

3    ENSRNOG00000007462 -1.421638

4    ENSRNOG00000004692 -1.519434

5    ENSRNOG00000002778  1.399885

6    ENSRNOG00000050057 -1.331353

7    ENSRNOG00000012939 -1.698565

8    ENSRNOG00000050860  2.288570

9    ENSRNOG00000002948 -1.437157

10   ENSRNOG00000010064 -1.699353

11   ENSRNOG00000036960 -1.405350

12   ENSRNOG00000005420 -1.603549

This does not work when uploaded throwing out the following error:

ERROR: The format of the uploaded ranked list is incorrect. Please make sure the file contains two columns of gene IDs and scores.

2. I tried converting the ENSEMBL rat gene ids to something more generic like gene symbols. Still the same error.

3. Finally, I did an experiment and ran the human example run, which works but when I copy and paste the data set into a text file and try to upload it as an RNK file, it does not work,  which would suggest some aspect of the uploading file process does not work. However, when I paste my own rat data it still does not play ball with me.

I'd be appreciative of any thoughts or advice. I have uploaded the original rank file and my r script as well as the test list (human genes)

Warm regards

Varun

[Yuxing Liao]

Hi Varun,

I think the problem is your header. Please remove the first line before submitting. You could use col.names=FALSE in write.table.

Yuxing

--
You received this message because you are subscribed to the Google Groups "webgestalt" group.
To unsubscribe from this group and stop receiving emails from it, send an email to webgestalt+...@googlegroups.com.
To post to this group, send email to webge...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/webgestalt/690805fe-c84f-4a4b-9ffc-a68d49bcfa3f%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Varun Venkatesh]

Solved! Thank you!

[Shiyang He]

Hi. Yuxing,

I encountered the same erro while uploading the .rnk file. But my files have only two columns (geneID and score).  Could please help me figure out how to run GSEA with my data?

The first 10 lines of my file is like:

Sox17   2.77799531080151

Mrpl15  0.99479859112523

Lypla1  1.34807409116277

Tcea1   0.664084467327668

Rgs20   1.29395534178585

Atp6v1h 1.3582767203676

Oprk1   -3.88579432553487

St18    -3.62521911175681

Pcmtd1  0.262655700265356

Sntg1   -4.09189941045295

To unsubscribe from this group and stop receiving emails from it, send an email to webge...@googlegroups.com.

[Shiyang He]

Solved. Thank you. I re write.table to the .rnk file and it worked. Last time I write all columns and select two columns with cut -f 1,3. I don't know what's the difference. 

[Dr. Jose Antonio Ruiz Perez]

Hello, I have the same problem, I have my file in rnk but the problem continues. 

To unsubscribe from this group and stop receiving emails from it, send an email to webge...@googlegroups.com.

[Shiyang He]

Your file is not right, line 14 and line 63  have no tab separator. I sovled this issue by using R write.table command to get the right format. 

[Dr. Jose Antonio Ruiz Perez]

Thank you very much, its running.