User: pkhadka

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pkhadka0
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Posts by pkhadka

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Comment: C: Batch correction with DeSeq2: problem with creating model and getting all condit
... I have actually used that function to do this before. I am just wondering if the normalized counts generated by DeSeq2 are batch corrected? And more importantly, are the DE genes that I get using the results function batch corrected? ...
written 7 weeks ago by pkhadka0
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Comment: C: Batch correction with DeSeq2: problem with creating model and getting all condit
... Thank you! Just another quick follow-up question: I want to get normalized counts corrected for the batch effect for all three conditions. I know that I can get normalized counts using "counts (dds, normalized=TRUE)", but I am not sure if the counts here is corrected for the batch effect? ...
written 7 weeks ago by pkhadka0
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Batch correction with DeSeq2: problem with creating model and getting all conditions
... I have RNAseq data for three conditions (A, B, and C) with results from three different batches (PK, GB, and EG) and I am trying to apply batch correction using DeSeq2. I am intersted in contrasting all three condtions (i.e. A vs B, B vs C and A vs C) while taking the batch effect into account. My c ...
deseq2 written 7 weeks ago by pkhadka0 • updated 7 weeks ago by Michael Love23k

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