Search
Question: Should I normalize communities separately with metagenomeseq?
1
gravatar for lilianeconteville
12 months ago by
lilianeconteville10 wrote:

Hello,

I have shotgun metagenomics data from fecal samples and my objective is to compare my data with shotgun metagenomic fecal data of three other communities already published.

For taxonomic analysis, I used Kraken (https://ccb.jhu.edu/software/kraken/) which gives me the raw number of reads that were assigned to each taxon. I am using metagenomeSeq to normalize the Kraken output and be able to compare the samples, however, I am wondering if I should normalize the samples separately, I mean, I wanna compare the gut microbiome of four human communities, so my question is if I should normalize the output of each community separately or not.

Thank you in advance, 

Liliane

ADD COMMENTlink modified 12 months ago by Joseph Nathaniel Paulson270 • written 12 months ago by lilianeconteville10
0
gravatar for Joseph Nathaniel Paulson
12 months ago by
United States
Joseph Nathaniel Paulson270 wrote:
I would do them together, though I guess it won't make much of a difference as the quantile chosen will likely fall to default and then you're calculating a sample specific scalar. On 2017-11-17 03:49, lilianeconteville [bioc] wrote: > Activity on a post you are following on support.bioconductor.org [1] > > User lilianeconteville [2] wrote Question: Should I normalize communities separately with metagenomeseq? [3]: > > Hello, > > I have shotgun metagenomics data from fecal samples and my objective is to compare my data with shotgun metagenomic fecal data of three other communities already published. > > For taxonomic analysis, I used Kraken (https://ccb.jhu.edu/software/kraken/) which gives me the raw number of reads that were assigned to each taxon. I am using metagenomeSeq to normalize the Kraken output and be able to compare the samples, however, I am wondering if I should normalize the samples separately, I mean, I wanna compare the gut microbiome of four human communities, so my question is if I should normalize the output of each community separately or not. > > Thank you in advance, > > Liliane > ------------------------- > > Post tags: metagenomeseq, microbiome, gut microbiome, metagenomics, shotgun metagenomics > > You may reply via email or visit Should I normalize communities separately with metagenomeseq? Links: ------ [1] https://support.bioconductor.org [2] lilianeconteville [3] Should I normalize communities separately with metagenomeseq?
ADD COMMENTlink written 12 months ago by Joseph Nathaniel Paulson270
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 189 users visited in the last hour