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@@ -582,6 +582,20 @@ Promoter counts in sliding windows around each gene's highest-expressed
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Results
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\end_layout
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+\begin_layout Standard
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+\begin_inset Note Note
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+status open
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+
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+\begin_layout Plain Layout
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+Focus on what hypotheses were tested, then select figures that show how
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+ those hypotheses were tested, even if the result is a negative.
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+\end_layout
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+
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+\end_inset
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+
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+
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+\end_layout
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+
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\begin_layout Itemize
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Different histone marks have different effective promoter radii
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\end_layout
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@@ -750,6 +764,30 @@ literal "true"
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\end_layout
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+\begin_deeper
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+\begin_layout Itemize
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+Note: Distinguish between the data set for the paper, using pre-generated
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+ fRMA vectors for standard array platform, vs.
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+ the other data set, generating custom tissue-specific fRMA vectors for
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+ niche platform.
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+\end_layout
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+
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+\begin_layout Itemize
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+Figure: MA plot, RMA vs fRMA, to show that the normalization is appreciably
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+ and non-linearly different
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+\end_layout
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+
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+\begin_layout Itemize
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+Figure MA plot, fRMA vs fRMA with different randomly-chosen sample subsets
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+ to show consistency
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+\end_layout
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+
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+\begin_layout Itemize
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+Figure showing trade-off between more samples per group and fewer groups
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+ with that may samples, to justify choice of number of samples per group
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+\end_layout
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+
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+\end_deeper
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\begin_layout Itemize
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voom, precision weights, and sva improved model fit
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\end_layout
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