Hello,
I would like to know what the differences are between the two summary statistics files on RNA expression between cases and controls: All Differential Expression (Merged)
(syn14237651) and Amp-AD Differential Expression Stats (syn27211942). Were the statistical models used in both the same? Could you provide a description of the newer dataset (i.e., syn27211942)?
I've noticed that the results between the two don't agree with each other for the genes I'm interested in.
Thank you in advance for your help with this.
Created by Lam-Ha Dang ldang Hi Lam-Ha,
I'm not sure of the exact difference between the two files in that rnaSeqReprocessing study -- syn27211942 was created much more recently though, and appears to be part of the analysis for the updated RNAseq Harmonization study that we just released. I think it may be in the old folder by mistake.
This new version of the study uses the same input data as the original rnaSeqReprocessing study, but with additional samples, some updates to the processing pipeline, and using the GRCh38 build for alignment. You can find the updated harmonized gene counts and DE results here: https://www.synapse.org/#!Synapse:syn21241740. The DE analysis was run using the sageseqr processing pipeline, which uses the `variancePartition::dream` function: https://sage-bionetworks.github.io/sageseqr/reference/differential_expression.html.
Let me know if you have other questions -- we anticipate that this will be a high-use dataset so we want to fill any missing info we can!
Abby
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