gct file error

[野口玲]

Dear Anthony,

Hi! 

I tried to prepare a gct file and gmt file for kinase activity assay to use ssGSEA 2.0 via R.

The previous gct file and gmt file worked well as attached file 1(input4_unique.gct) and 2 (pmt_uni.gmt). 

Following the successful gct file, I prepared new gct file as an attached file 3 (input_ssgsea_bus_unique.gct).

I tried to perform ssGSEA2.0 using the new gct file and the previous generated gmt file in R.

However, the new gct file got an error message.

Would you like to tell me a solution of the error message ?

Many thanks,

Rei 

[Castanza, Anthony]

Hi Rei,

Could you send the specific text of the error message? ssGSEA for PTMSigDB is produced by one of our collaborators, so depending on what the exact problem was, it may or may not be beyond my ability to help and you might need to reach out to them directly through their github.

 

-Anthony

 

Anthony S. Castanza, PhD

Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/78fc36aa-ad0d-452b-bece-66a17f374901n%40googlegroups.com.

 

[野口玲]

Dear Anthony,

Thanks for your quick reply.

I'm sorry to forget to send the error message to you.

Following message is the error message.

> source("~/ssGSEA2.0-master/ssgsea-gui.R")
Running ssSGEA on: ssGSEA_data_JO_bos_unique.gct 

parsing as GCT v1.3
C:\Users\user\Documents\ssGSEA2.0-master\data/ssGSEA_data_JO_bos_unique.gct 116 rows, 3 cols, 0 row descriptors, 0 col descriptors
Error in ssGSEA2(input.ds, gene.set.databases = gene.set.databases, sample.norm.type = sample.norm.type,  : 
  object 'm' not found
In addition: Warning message:
In matrix(mat, nrow = nrmat, ncol = ncmat + nrhd + col_offset, byrow = TRUE) :
  data length [456] is not a sub-multiple or multiple of the number of rows [116]
Error in exists(cacheKey, where = .rs.WorkingDataEnv, inherits = FALSE) : 
  invalid first argument

Many thanks,
Rei 

2023年8月23日(水) 6:44 Castanza, Anthony <acas...@cloud.ucsd.edu>:

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/F1D75803-D031-463F-AB89-B8E88F458834%40hxcore.ol.

[Castanza, Anthony]

Hi Rei,

Based on this error message, it looks like there is an issue with your GCT formatting. It appears that you’ve used the GCT 1.3 spec, which is slightly more complicated, however, since you don’t have additional row or col descriptors (0 and 0 in the message below, and in the file header you sent before), I might suggest reformatting it to the simpler 1.2 specification, and double checking that your row and column counts are correct and that there aren’t any invisible rows (you should be able to check this in a plain text editor).

GCT 1.2 format here: https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29

 

Let me know if you still have issues here after attempting to correct the file formatting.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/CA%2Ba0%2B7%2BF2NgrHFBWrWumxoYgR-wkfHcd%2B5jZM6Q5%3Df2Ho-1k1g%40mail.gmail.com.

 

[野口玲]

Dear Anthony,

Thanks for your reply.

As following your advice, I changed the file format from GCT 1.3 to GCT 1.2.

Successfully, the file worked well.

I appreciated your help.

After checking the output data, I have one question.

The row numbers of my input file were little compared with the phospho--proteomics data and RNA-Seq data.

Therefore, the row numbers of output files were very few.

How do I interpret the output file ?

 Would you like to tell me the meaning of id as an attached file ?

I would like to know kinases which id includes.

Many thanks,

Rei 

2023年8月26日(土) 3:45 Castanza, Anthony <acas...@cloud.ucsd.edu>:

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/35FAEE2B-15F8-47BA-A711-BEF71DED51BA%40hxcore.ol.