Better to use tximport instead of manually rounding off.
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poisonAlien
PCA from kallisto output
Hi,
My goal is to plot a simple PCA to compare samples after kallisto run.
I am a bit confuse how to do it. Should I take the "est_counts" or the "TPM" values ?
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Picasa
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My lab takes the estimated counts, rounds them to the nearest integer, performs VST normalization using the DESeq2 package, then plots the first two PC coordinates from the prcomp() function.
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Just taking into consideration what the package
rnaseqGenehas to say, I would use normalized data to to a PCA. Hope it helps :)From what I understand, TPM is already normalized no ?
The package you mentioned seems to recommend to apply
rlogon counts data.