In the IVY GAP RNAseq data, I have downloaded and checked the spreadsheets for what I believe to be all of the Leading Edge and Pseudopalisading differential expression data, and all of the MRI coordinates appear to be -1, which I understand to mean there is no MRI coordinate data for the dataset. Does any of the data actually contain MRI coordinates? If so, could you direct me to it? Thank you!

Dear AustinKunch,

The Ivy GAP does not have any data based on region, ISH, tissue block, or LMD-RNA-Seq sample that is tied to MRI coordinates. In other Allen Institute atlases, -1 is typically used to represent coordinates with no data (e.g., locations with no anatomical coordinates). There are other users of the Ivy GAP who have attempted to map the histology data, or at least tissue block, to the MRIs, but I am not sure what the status is of these efforts. As I explained to Qin in this forum’s same topic, accurate mapping probably cannot be achieved without multiple stereotactic biopsy MRIs for each patient, which was not done for the Ivy GAP.

Thank you,

Ralph

Hi Ralph,

Thank you for your help!

Also, I have looked on the forum a bit and read through the documentation and haven’t found an answer to this question, so I assume the answer is very obvious. What do z score values of exactly 0 in the IVY GAP downloadable data mean? Do they either mean that there is a missing data point or that the z score was actually exactly zero?

Thank you,

Austin Kunch