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@@ -1246,7 +1246,7 @@ literal "false"
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\end_layout
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\begin_layout Subsection
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-RNA-seq align+quant method selection
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+RNA-seq align+quant method comparison
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\end_layout
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\begin_layout Standard
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@@ -1254,7 +1254,7 @@ RNA-seq align+quant method selection
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status open
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\begin_layout Plain Layout
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-Maybe fix up the axis ranges for these plots?
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+Maybe fix up the excessive axis ranges for these plots?
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\end_layout
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\end_inset
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@@ -1415,7 +1415,7 @@ Comparison of quantification between STAR and Salmon for identical annotation
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\begin_inset Float figure
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wide false
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sideways false
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-status open
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+status collapsed
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\begin_layout Plain Layout
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\align center
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@@ -1452,7 +1452,7 @@ n
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\begin_inset Float figure
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wide false
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sideways false
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-status open
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+status collapsed
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\begin_layout Plain Layout
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\align center
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@@ -1485,14 +1485,198 @@ Comparison of quantification between Salmon with and without Shoal for identical
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\end_layout
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-\begin_layout Standard
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-
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+\begin_layout Itemize
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+Ultimately selected shoal as quantification, Ensembl as annotation.
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+ Why? Running downstream analyses with all quant methods and both annotations
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+ showed very little practical difference, so choice was not terribly important.
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+ To note in discussion: reproducible workflow made it easy to do this, enabling
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+ an informed decision.
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\end_layout
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\begin_layout Subsection
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RNA-seq has a large confounding batch effect
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\end_layout
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+\begin_layout Standard
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+\begin_inset Float figure
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+wide false
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+sideways false
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+status open
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+
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+\begin_layout Plain Layout
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+\align center
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+\begin_inset Graphics
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+ filename graphics/CD4-csaw/RNA-seq/weights-vs-covars-CROP.png
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+ lyxscale 25
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+ width 100col%
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+ groupId colwidth-raster
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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 Plain Layout
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+\begin_inset Caption Standard
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+
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+\begin_layout Plain Layout
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+
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+\series bold
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+\begin_inset CommandInset label
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+LatexCommand label
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+name "fig:RNA-seq-weights-vs-covars"
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+
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+\end_inset
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+
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+RNA-seq sample weights, grouped by experimental and technical covariates
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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 Plain Layout
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+
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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 Standard
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+\begin_inset Float figure
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+wide false
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+sideways false
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+status open
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+
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+\begin_layout Plain Layout
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+\align center
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+\begin_inset Graphics
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+ filename graphics/CD4-csaw/RNA-seq/PCA-no-batchsub-CROP.png
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+ lyxscale 25
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+ width 100col%
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+ groupId colwidth-raster
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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 Plain Layout
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+\begin_inset Caption Standard
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+
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+\begin_layout Plain Layout
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+
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+\series bold
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+\begin_inset CommandInset label
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+LatexCommand label
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+name "fig:RNA-PCA-no-batchsub"
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+
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+\end_inset
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+
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+RNA-seq PCoA plot showing clear batch effect
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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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+\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 Standard
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+\begin_inset Float figure
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+wide false
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+sideways false
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+status open
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+
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+\begin_layout Plain Layout
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+\align center
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+\begin_inset Graphics
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+ filename graphics/CD4-csaw/RNA-seq/PCA-naive-batchsub-CROP.png
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+ lyxscale 25
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+ width 100col%
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+ groupId colwidth-raster
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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 Plain Layout
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+\begin_inset Caption Standard
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+
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+\begin_layout Plain Layout
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+
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+\series bold
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+\begin_inset CommandInset label
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+LatexCommand label
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+name "fig:RNA-PCA-no-batchsub-1"
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+
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+\end_inset
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+
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+RNA-seq PCoA plot showing clear batch effect
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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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+\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 Standard
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+\begin_inset Float figure
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+wide false
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+sideways false
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+status open
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+
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+\begin_layout Plain Layout
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+\align center
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+\begin_inset Graphics
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+ filename graphics/CD4-csaw/RNA-seq/PCA-combat-batchsub-CROP.png
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+ lyxscale 25
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+ width 100col%
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+ groupId colwidth-raster
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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 Plain Layout
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+\begin_inset Caption Standard
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+
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+\begin_layout Plain Layout
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+
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+\series bold
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+\begin_inset CommandInset label
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+LatexCommand label
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+name "fig:RNA-PCA-no-batchsub-2"
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+
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+\end_inset
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+
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+RNA-seq PCoA plot showing clear batch effect
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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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+\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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RNA-seq batch effect can be partially corrected, but still induces uncorrectable
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biases in downstream analysis
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