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trouble shoots in GEOexplorer running #46

Open 2559341252 opened 1 year ago

2559341252 commented 1 year ago

I tried to use GEOexplorer for comprehensively identifying RNA (lncRNA, CirRNA, miRNA, and mRNA) in exosomes of plasma from gestational diabetes. Searching in GEOexplorer with key words “exosome GDM”, I got 17 entries. Only two of them (GSE192813, GSE114860) could be accepted by GEOexplorer. So I did the analysis of the two datasets.

  1. While I was putting GSE192813 (platform: GPL16791) and running “Dataset information-Experiment information-Analyse”, a note“The experimental conditions information row names do not match the count matrix column names. Therefore the count matrix column names will be displayed in the experimental conditions information tables.”was presented. Furthermore, the “Experimental conditions information” did not show entire data. This made “Select the experimental conditions to include in Group 1” or “Select the experimental conditions to include in Group 2” impossible and failed to go forward the analysis.
  2. While I was trying the other dataset GSE114860, the “Error: An error has occurred. Check your logs or contact the app author for clarification.” was shown in the “Apply log transformation to the data:” and the analysis was stopped at the “dataset information”. I attempted to rebuild GEOexplorer dataset following the “Tutorial”. Unfortunately, I could not find the “.txt” file for download in GEO.
  3. GEOexplorer did not recognize the GEO accession codes with GSM “GSMXXXXXXX”, I also tried to rebuilt GEOexplorer datasets by using “Gene Expression File Template”. Again, no “.txt” file available for download in GEO. I got frustration with GEOexplorer and wondering how I can go forward. Were there bugs in my computer or problems of the uploaded datasets by authors in GEO database? Thank you very much for your help in advance.
guypwhunt commented 1 year ago

Hello

Sorry about the slow reply, it has been a busy week and thank you for using GEOexplorer.

I know exactly the issue you are facing and honestly, it is one of GEOexplorer's biggest limitations. It all comes down to the fact that RNA-seq datasets stored on GEO are in such a huge variety of formats that it is a bit touch and go whether GEOexplorer can use them automatically or if the files need to be manually formatted first.

I have formatted both the datasets you mentioned and tested them out on the website version of GEOexplorer.

GSE192813_experimental_conditions.csv GSE192813_expression_data.csv GSE114860_expression_data.csv GSE114860_experimental_conditions.csv

The GSM codes from the search relate to columns within a dataset rather than the entire dataset, so they can't really be used on their own without the rest of the dataset if that makes sense.

Let me know if you need a hand formatting any more datasets or if there is any other way I can help.

Have a lovely weekend.