I just want to make sure that I fully understand the provided HBTRC prefrontal cortex Agilent 44K expression data (AMP-AD_HBTRC_MSSM_Agilent44Karray_PFC_AgeCorrected_all.tsv).
The data represented here is log10 (Cy5/Cy3) test/reference, with the reference being used for each sample. This expression data is has been corrected by principal components that correspond to 2 classes of control probes: 1) specialty technical probes like spike-ins and 2) edge probes. Then, the data was corrected with biological covariates by residuals from linear model fitting incorporating:RIN, pH, postmortem interval, age, array batch, preservation, and gender.
If you could confirm that the AMP-AD_HBTRC_MSSM_Agilent44Karray_PFC_AgeCorrected_all.tsv is log10 test/reference and was corrected by control probe as well as biological covariates, that would be a big help.
Created by Shaun Grosskurth Segrossk2015 Thanks for confirming Mette. I did go to the methods of the Zhang et al paper to supplement the methods provided on Synapse for how the Agilent data was transformed/normalized. By the way, the Agilent gene expression data did not have much structure for any covariate when I performed sample quality control (correlation plot, PCA, tSNE, hierarchical cluster). Hi Shaun,
This release is a subset of the data reported in the Zhang et al., paper. Please see here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677161/
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