User: adityabandla

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adityabandla10
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Posts by adityabandla

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Transforming Variance Stabilised Counts to Relative Abundances
... For my metagenomics dataset, I would like to retain only genes that are are >0.1% in abundance, for plotting and for subsetting differentially abundant genes I applied VST on the raw counts. Is it OK to convert variance stabilised counts to relative abundances? or is it better to do this filteri ...
deseq2 written 13 months ago by adityabandla10 • updated 13 months ago by Wolfgang Huber13k
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Comment: C: Setting up Experiment Design in baySeq
... Thanks Tom for the detailed insight! I think I will take your advise on comparing the categorical variables within each site separately and then combine the posterior likelihoods for each gene of interest Thanks once again ...
written 13 months ago by adityabandla10
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Setting up Experiment Design in baySeq
... I have a metagenomics dataset, gene counts (rows) x samples (columns). I am trying to find out genes that are differentially abundant across different levels of my categorical variable of interest. I have already performed this analysis using DESeq2, however I would like to compare my results with b ...
bayseq written 13 months ago by adityabandla10 • updated 13 months ago by Thomas J Hardcastle170
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Comment: C: Possible to calculate odds ration using DESeq2?
... Thanks Michael! I'm sorry if my question is naive, I have been trying to wrap my head around this. Is it possible to calculate the log odds of a gene being enriched/log odds for a given log2foldchange for pairwise comparisons? ...
written 13 months ago by adityabandla10
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Possible to calculate log odds using DESeq2?
... I have a metagenomics dataset, which essentially is a counts matrix (genes as rows and samples as columns). One of my objectives was to identify differentially abundant genes across my sample groups, which I did using DESeq2 I am wondering if its also possible to do some qualitative testing, based ...
limma deseq2 written 13 months ago by adityabandla10

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