Delete some obsolete TODOs

thesis.lyx

@@ -1013,34 +1013,6 @@ name "sec:Biological-motivation"
 Biological motivation
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-Find some figures to include even if permission is not obtained.
- Try to obtain permission, and if it cannot be obtained, remove/replace
- them later.
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-Rethink the subsection organization after the intro is written.
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 Rejection is the major long-term threat to organ and tissue allografts
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@@ -6479,23 +6451,6 @@ Result of RNA-seq batch-correction using MOFA latent factors
 Results
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-Focus on what hypotheses were tested, then select figures that show how
- those hypotheses were tested, even if the result is a negative.
- Not every interesting result needs to be in here.
- Chapter should tell a story.
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 Interpretation of RNA-seq analysis is limited by a major confounding factor
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@@ -7471,19 +7426,6 @@ noprefix "false"
  histones.
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 All 3 histone marks tend to occur more often near promoter regions, as shown
  in Figure 
@@ -10164,20 +10106,6 @@ Gene expression grouped by promoter coverage clusters.
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-Repeated figure legends are kind of an issue here.
- What to do?
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@@ -10400,19 +10328,6 @@ I forgot until recently about the work I did on this.
 Discussion
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-Write better section headers
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 Each histone mark's 
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@@ -11412,32 +11327,6 @@ MACS
 y.
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-Data quality issues limit conclusions
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-Is this needed?
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 Future Directions
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@@ -12243,10 +12132,15 @@ Fill this out
 Arrays for diagnostics
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 Arrays are an attractive platform for diagnostics
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 Proper pre-processing is essential for array data
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@@ -14022,32 +13916,6 @@ literal "false"
 Results
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-Improve subsection titles in this section.
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-Reconsider subsection organization?
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 Separate normalization with RMA introduces unwanted biases in classification
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@@ -17037,20 +16905,6 @@ wide false
 sideways false
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-Consider transposing these tables
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 wide false
@@ -18624,20 +18478,6 @@ SVA
 Future Directions
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-Some work was already being done with the existing fRMA vectors.
- Do I mention that here?
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 Improving fRMA to allow training from batches of unequal size
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@@ -21662,27 +21502,6 @@ GB
  expression.
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 The data do indeed show small systematic perturbations in gene levels (Figure
  
@@ -21889,19 +21708,6 @@ edgeR
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-Give these numbers the LaTeX math treatment
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