Differential abundance analysis of two samples with only a single replicate
Dear All,
I am trying to perform a differential abundance analysis of two sets of samples (Samples A and B), in which they approximately share 20 OTUs.
However, I only have 2 replicates for Sample A, and 1 replicate for sample B.
I will like to find out which OTUs are more quantitatively abundant between the two samples. I have read that DeSeq2 is not possible because I will require replication. Some have recommended R-log transformation.
Are there other ways to go ahead doing this? I was thinking fold-change between the OTU is one method. Will appreciate any feedback or comments.
Thank you!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Appropiate normalization method for OTU table built from MAGs abundances estimations?
written by v.berriosfarias •
-
How to do diferential expression analysis of 2 closely related species
written by Fernando •
-
How can I do hypothesis test for continuous dependent variable and two categorical independent vari…
written by BioDH •
-
Log transformation of relative abundance to visualize difference in small numbers for a heatmap
written by almogangel •
-
LEFSE: Should I remove features with low relative abundance or lefse will take care of it?
written by deep771992chanda •
-
Perform two-way ANOSIM in R
written by vin.darb
-
How do I look for shared OTUs in an abundance matrix?
written by Ming •
-
How to quantitative identification outlier from technology replication and biological replication
written by Grace_G •
-
Change OTU names to taxon names
written by mollysil •
-
Removal of rare OTUs before calculating community distances / ADONIS / NMDS
written by dmcleanuk •
In your own mind, is this a statistically valid experimental setup? You could analyse the 2 samples, but what would it mean? Which journal would accept the work for publication?