User: rpolicastro
rpolicastro • 720
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Posts by rpolicastro
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Comment:
C: Assessing controls for RNASeq
... When doing differential expression, you could include batch as an additional variable in your regression model `~ condition + batch`. The regression model will at the same time help to control for batch effect, and also let you test which genes are differential expressed between batches. ...
written 2 hours ago by
rpolicastro • 720
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... The reason `integratedexpression.filtered <- integratedexpression[DEGs.genes, ]` is not working now is because not all of the genes you are trying to subset are in the rownames of the matrix. You can ignore the genes that are absent by instead doing this.
integratedexpression.filtered <- ...
written 1 day ago by
rpolicastro • 720
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... What information are you trying to get across with the plot? ...
written 1 day ago by
rpolicastro • 720
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... I can't remember 100% off the top of my head, But I think all of the RNA slots, as well as the counts and data slots of SCT contain all genes that pass quality filtering. On the other hand, SCT scale.data, and all (or most) of the integration assay slots only have the top 2-3k most variables genes. ...
written 1 day ago by
rpolicastro • 720
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... When you did the marker analysis, what assay and slot did you use? Some of the slots hold all genes that pass quality filtering, while others only hold the top 2-3k most variable genes. ...
written 1 day ago by
rpolicastro • 720
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... The [ggpubr library](https://github.com/kassambara/ggpubr) has a convenience function to make a box plot with significance bars. ...
written 1 day ago by
rpolicastro • 720
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Comment:
C: heatmap for TCGA kirk data
... You should put the code you are using here so we know what you are doing. Preferably a reproducible example using a smaller chunk of your data. ...
written 2 days ago by
rpolicastro • 720
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... I find that the scRNA-seq dim plots will sometimes melt illustrator as well. I found a handy library, ggraster, that will let you rasterize the points but keep the labels and such as vectors. I figured I would pass this along in case you haven't seen it. ...
written 2 days ago by
rpolicastro • 720
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... That's a really handy wrapper for pheatmap, thanks for sharing! ...
written 2 days ago by
rpolicastro • 720
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... ComplexHeatmap has a [long but detailed vignette](https://jokergoo.github.io/ComplexHeatmap-reference/book/) that you can go through.
Your can prepare your count matrix with this code. Put the genes you want to include the the genes vector.
library("Seurat")
counts <- GetAssyData(s ...
written 2 days ago by
rpolicastro • 720
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