R Package: AnnotateGeneData function not working properly


When running the ExpressAnalystR package in RStudio for meta-analysis, executing ReadOmicsData and SanityCheckData functions works perfectly fine, however, when running the AnnotateGeneData function, the data.annotated nested list within my dataset object, has a “” as value.

Furthermore, when I run ReadOmicsData on my datasets, folders get created that are named [DATASET NAME].csv/txt_data, and that folder contains a file called data.raw.qs.

To elaborate further, when I try to run the AnnotateGeneData function, the annotation files are correctly downloaded along with the hsa.genes.sqlite file.

However, none of my files found within the dataSet object have any annotations under data.annotated.
Due to this, when I try to run the RemoveMissingPercent function on my loaded datasets, I get the following error message:

Error in qs::qread(file = paste0(dataName, “_data/”, name)) :
Failed to open file for reading.

  • Does the file exist?
  • Do you have file permissions?
  • Is the file name long? (usually 255 chars)

This makes sense, since the annotation has not been performed successfully. However, I have no idea how to go about solving this issue. Any ideas? PlotDataProfile seems to work perfectly fine once the datasets are loaded to the dataSet object, but there seems to be a problem with the annotation function.

Could you share with me your datasets so I checkout what is wrong?