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hagenaue / FrontalPole_Microarray

Reanalysis of public frontal pole (BA10) microarray data to accompany our qPCR project examining neurotransmission-related gene expression in the frontal pole in relationship to Bipolar Disorder and Schizophrenia.
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Comparisons w/ previous DLPFC results #16

Open hagenaue opened 3 years ago

hagenaue commented 3 years ago

We should compare our BA10 microarray & meta-analysis results to previous results from large studies in the DLPFC, including:

1) The huge Gandal et al. 2018 cortical microarray meta-analysis.

2) The huge Gandal et al. 2018 DLPFC RNA-Seq meta-analysis.

3) Microarray results derived from grey-matter only DLPFC dissections. For this, we can use the output from my re-analyses of Lanz and Narayan's datasets that were included in the PLOS cell type paper (Hagenauer et al. 2018).

4) If we want to compare the results for other variables in our dataset (age, pH, PMI, gender) to what has been seen before, we can use the output from my analyses of the Pritzker DLPFC data that were included in the PLOS cell type paper (Hagenauer et al. 2018).

hagenaue commented 3 years ago

To do this, I need to first:

1) Update my original code comparing Adriana's results to the DLPFC results to:

A) Include the Gandal meta-analysis results (instead of the earlier CMC results) - this will require converting the ENSEMBL annotation to Gandal to something shared with the other datasets (Gene Symbol, Entrez)

B) Join the data-frames using "match=all" instead of "match=first"

C) Include code for the comparison scatterplots (vs. making them by hand in Excel - yuck!)

hagenaue commented 3 years ago

... then I can pass that code to you, and you can doctor it to run a BA10 microarray vs. DLPFC comparison.