search

ISA-tools / MAGEtoISAconverter

Converter which can pull from ArrayExpress (by an accession number) or read local files and convert them to ISAtab. Lead by Philippe Rocca-Serra & Eamonn Maguire, University of Oxford
http://isa-tools.org
7 stars 2 forks source link

Missing Assay Files #16

Closed psm3426 closed 11 years ago

psm3426 commented 11 years ago

Hello,

I just tried out the new parser, and I've noticed that there are some studies that seem to be successfully converted (no error messages), but have missing assay files. In the investigation file, there will be multiple assay files listed in the Study Assay section, but no corresponding files exist after conversion.

Some examples are E-MTAB-857, E-GEOD-15292, E-GEOD-28833, and E-ERAD-12.

I'm not really sure why this happens.

eamonnmag commented 11 years ago

This is most likely down to unrecognised assay types. The way of describing assays is inconsistent within mage-tab so we had to write a lot of checks in for the different types. Will look in to this.

psm3426 commented 11 years ago

Thank you!

proccaserra commented 11 years ago

Hi Psalm,

I just checked E-GEOD-28833, and E-ERAD-12 and i have missed possible values used by ArrayExpress (MBD-Seq) or inconsistent use (for instance using "non-genomic" for library source and other for library strategy in the former when RNA-Seq is used.

It is a similar situation for E-GEOD-15292 and E-MTAB-857 was not available tonight

I'll push the fix asap

thanks for reporting the issue and sorry for the inconvenience

Best

Philippe

On 24/09/2012 22:22, psm3426 wrote:

Hello,

I just tried out the new parser, and I've noticed that there are some studies that seem to be successfully converted (no error messages), but have missing assay files. In the investigation file, there will be multiple assay files listed in the Study Assay section, but no corresponding files exist after conversion.

Some examples are E-MTAB-857, E-GEOD-15292, E-GEOD-28833, and E-ERAD-12.

I'm not really sure why this happens.

— Reply to this email directly or view it on GitHub https://github.com/ISA-tools/MAGEtoISAconverter/issues/16.