User: Sachin Pundhir

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Posts by Sachin Pundhir

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Comment: C: DESeq2 PCA plot on fitted values
... Thanks, based on the suggestion, I made two PCA plots (https://www.dropbox.com/s/nk55yr1cgvux6hr/DESeq2_pca_plot.pdf?dl=0)   a) on normalized read counts plotMDS(log(counts(dds, normalized=TRUE) + 1)) b) on the difference between the counts and fitted values   plotMDS(log(counts(dds, normaliz ...
written 4.6 years ago by Sachin Pundhir0
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DESeq2 PCA plot on fitted values
... I am analyzing a RNA-seq data having some batch effect using DESeq2. To account for the effect, I add it as a covariate to the regression model. Next, to determine, how well the effect is corrected, I plot two PCA plots 1. plotMDS(assays(dds)[["counts"] ] - raw count 2. plotMDS(assays(dds)[["mu ...
deseq written 4.6 years ago by Sachin Pundhir0 • updated 4.6 years ago by Michael Love24k

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Popular Question 4.6 years ago, created a question with more than 1,000 views. For DESeq2 PCA plot on fitted values

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