Error 1005

[Mehri]

I'm having trouble with running the data. it sends  error 1005. I chose collapse and ensemble gene v7.5.1. attached is the screen shot of my phenotype and expression data. I 'd appreciate your help. Thanks

[Anthony Castanza]

Hi Mehri,

The issue here would appear to be the decimal versions after the ensembl gene base ID, e.g. the ".6" after the "ENSG00000123456". These versions can be removed using the text to columns tool in excel by splitting on the ".".

Additionally, for human rna-sequencing data we recommend changing the "collapse mode for probe sets >=1" under advanced fields from the default "Max_probe" to "Sum_of_probes".

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

On Thu, Jan 27, 2022, 7:49 AM Mehri <drmona...@gmail.com> wrote:

I'm having trouble with running the data. it sends  error 1005. I chose collapse and ensemble gene v7.5.1. attached is the screen shot of my phenotype and expression data. I 'd appreciate your help. Thanks

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[Mehri]

I am having another problem. there is a warning that says " There were 31420 row(s) in total with partially missing data in this dataset". I attached the screen shot which shows that one of my replicates doesn't show any values. Thanks for your help.

[Anthony Castanza]

Hi Mehri,

 

That is very odd, it looks like when it parsed the GCT it lost the data from one of the P0 samples. I might suggest opening the gct file in a plain text editor and making sure that everything still looks in-line with the GCT specification (i.e. no extra tabs between samples).

If you're willing to send us the files we can take a look and try to figure out what might've gone wrong here. You can send the gct and cls file to gsea...@broadinstitute.org confidentially and we'll take a look.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

 

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[Mehri]

the columns were messed up in text document I could fix it. thanks for your help.