Question: DESeq2 for 16S rRNA
0
gravatar for tegan.sutton
7 months ago by
tegan.sutton0 wrote:

Hi,

I'm new to this so apologies if my question is very simple....

I conducted DESeq2 anlaysis for some 16S rRNA sequencing data. I compared the differentially expressed genes between two time points.

Example results for one OTU is below, so a log2 fold increase of 24.2 from timepoint 1 to 2. Please can someone explain what this actually means? And also what the base mean is?

My supervisor made this comment and now i am unsure of what my results are actually saying - "I think you are referring to a 24 fold increment in numbers aren’t you or is the start log 0.1? If for example they start at log 2.0, or 100 cfu/g, then a 24 fold increment would take it to log 48. It may be more useful to identify where you are going to and from where – eg log 1 to log 6 – as this is more interpretable".

OUT baseMean = 17.61369762
log2FoldChange = 24.21197847 lfcSE = 1.796033089 stat =13.48080869 pvalue = 2.03E-41 padj = 6.84E-38 Genus = Veillonella

If someone could get abck to me ASAP, id be so grateful :)

deseq2 • 126 views
ADD COMMENTlink modified 7 months ago by Michael Love25k • written 7 months ago by tegan.sutton0
Answer: DESeq2 for 16S rRNA
1
gravatar for Michael Love
7 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Please when asking for support for open source software refrain from asking for it ASAP. We provide support when we can but typically it’s outside of our usual hours doing primary research.

Probably this LFC is from a gene where one group has no positive counts. Take a look at your data, either in the console or with plotCounts.

Also in the DESeq2 vignette we show how to compute and visualize posterior LFCs. Many of your questions are answered in the vignette and help pages for specific functions.

ADD COMMENTlink written 7 months ago by Michael Love25k
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