Hi @ajdefreese ,
There are a few Community Forum threads on this topic already. A good one to start with would be this one: Transcriptomics (RNA-seq/microarray) data normalization - FAQ . The short answer is that it likely has to do with the way data is summarized or normalized on the website relative to the raw data download. If you are comfortable working with the downloaded data, I’d recommend using those values and associated statistics in your analysis.
Best,
Jeremy