DESeq normalization
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nafsa • 0
@05efe0b6
Last seen 10 weeks ago

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Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session

sessionInfo( )
Hi, Id like to normalize my dataset with DESeq2. I make the DESeq object with : dds = phyloseq_to_deseq2(ps, Design) followed by deseq_counts_vst = varianceStabilizingTransformation(dds).
And I get error saying every gene contains at least one zero, cannot compute log geometric means.
Now i want to use pseudocount. Although I dont know how to write the script. Could you please help?

flowCHIC • 135 views
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@mikelove
Last seen 47 minutes ago
United States

In my opinion, this type of data is not appropriate for DESeq2 scaling methods (or inference), which are developed for RNA-seq. If there are no genes without a zero, the median ratio method will not work.