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Question: DESeq2 on 16S copy number corrected genes
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gravatar for ghanbari.msc
11 weeks ago by
ghanbari.msc10
ghanbari.msc10 wrote:

Hi 

I am currently working on some metagenome data and I'd like to use DESeq2 tool to find the genes that are differentially abundant in different treatment over time. Due to the type of the study, I need to normalize the count data (genes abundance) per 16S rRNA copy number which changes the distribution and nature of data from count to decimal. I know that DESeq2 works on the count data but I was just wondering if there is any possible way to analyze my data using DESeq2?

I'd appreciate the comments.

Mehdi

ADD COMMENTlink modified 11 weeks ago by Michael Love15k • written 11 weeks ago by ghanbari.msc10
1
gravatar for Michael Love
11 weeks ago by
Michael Love15k
United States
Michael Love15k wrote:

hi Mehdi,

The way to normalize in DESeq2 if you have a matrix is to not divide the counts, but to provide this matrix to estimateSizeFactor's normMatrix argument (see the help page for estimateSizeFactors). You should divide out the geometric mean of each row of your matrix before providing it to estimateSizeFactors.

ADD COMMENTlink written 11 weeks ago by Michael Love15k

Thanks Michael for the reply. I have the number of 16S copy per sample but I do not know how to create a matrix out of it. The data are like this:

                    Sample1 Sample2    Sample3 ......

16S copy      2000         1500         1000     ......

Do you have a suggestion on how to create a matrix from this?

I'd appreciate your comments.

Mehdi

 

 

ADD REPLYlink written 11 weeks ago by ghanbari.msc10

hi Mehdi,

It's not really a specialty of mine, so I don't have any ideas what the right analyses here are.

ADD REPLYlink written 11 weeks ago by Michael Love15k
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