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LieberInstitute / spatialLIBD

Code for the spatialLIBD R/Bioconductor package and shiny app
http://LieberInstitute.github.io/spatialLIBD/
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Trouble loading two gene sets #39

Closed abspangler13 closed 2 years ago

abspangler13 commented 2 years ago

I'm having trouble with two of the gene sets.

The loaded Scatterstrom data doesn't have the correct column names. Here's the code I run and here's the error I get when trying to create asd_exome_geneList.

https://github.com/LieberInstitute/spatialDLPFC/blob/5790c2673cd1661bda7169451f1b75875899fd43/code/analysis/10_Clinical_Gene_Set_Enrichment/01_Clinical_Gene_Set_Enrichment.R#L78-L91

image

The second gene set doesn't load and I believe it to be a permissions problem. Here is the code I ran to load the data:

https://github.com/LieberInstitute/spatialDLPFC/blob/5790c2673cd1661bda7169451f1b75875899fd43/code/analysis/10_Clinical_Gene_Set_Enrichment/01_Clinical_Gene_Set_Enrichment.R#L172-L175

And here is the error message:

image

lcolladotor commented 2 years ago

This issue was for this repo https://github.com/LieberInstitute/spatialDLPFC/issues/111 not for spatialLIBD. In any case, after our meeting on Thursday, this got resolved.