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cchen22 / TIGER

Transcriptional Inference using Gene Expression and Regulatory data
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Error with running the model on the provided data #1

Open loganminhdang opened 1 year ago

loganminhdang commented 1 year ago

Hey, thanks for creating this package.

Understand that this is a highly experimental tool and bugs are to be expected. I tried replicating your code (using your data) but was given the following error:

Unrecoverable error evaluating the log probability at the initial value. Exception: to_matrix(matrix): rows columns (398720) and vector size (398496) must match in size (in 'C:/Users/ADMIN/AppData/Local/Temp/RtmpA1tsWr/model-7cc63982bb9.stan', line 65, column 2 to column 37) Chain 1 Exception: to_matrix(matrix): rows columns (398720) and vector size (398496) must match in size (in 'C:/Users/ADMIN/AppData/Local/Temp/RtmpA1tsWr/model-7cc63982bb9.stan', line 65, column 2 to column 37) Warning: Fitting finished unexpectedly! Use the $output() method for more information.

Error: Fitting failed. Unable to retrieve the draws.

The same error occurred when I ran the model on both my own data and other databases of Dorothea. Can you please advise?

cchen22 commented 1 year ago

Hey @loganminhdang Thanks for your interest in TIGER!

Hmm, this error is strange. It looks like the product of the number of transcription factors and target genes doesn't match the size of elements in the regulatory network. I can't reproduce this error using my test data "TIGER::expr" and "TIGER::prior". Could you provide your R code and the full output in R for me to take a look?

Thanks, Chen