How to correctly interpret ALDEx2 output - differential abundance testing
1
0
Entering edit mode
RvH • 0
@9e983fb2
Last seen 14 months ago
Netherlands

Dear Community,

I'm running an ALDEx2 analysis in R on microbiome data and I'm currently wondering if I'm interpreting the data correctly.

code I run for the AldeX2 analysis:

aldexmodel <- aldex(Aldex_mat_fungi_antago, Aldex_variable_fungi_location_antago, mc.samples=128, test="t", effect=TRUE,include.sample.summary=TRUE , denom="all", verbose=FALSE)

The 'treatment' to be tested is "location" which consists of 2 possiblities: "front" or "back".

In the model output I can see that I have 2 Features/ASVs with a P-value <0.05 according to the Welsh t-test (we.ep, in output).

I know which 2 features this are, but I want to know if they are more present in the "back" or "front". Therefore I think I need to check the "rab.win" values, shown in the image below (the 2 features are highlighted in yellow):

enter image description here

feature 1 (ending with ...721) has a rab.win value of 0.88 for the 'back' and -6.53 for the front. Do I interpret correctly that this feature is more abundant in "back"

feature 2 (ending iwth ....15db) has a rab.win.back value of -6.9 and a rab.win.front value of 1.94. Do I interpret correctly that this feature is more abundant in "front"?

So the higher the 'rab.win.back' value, the higher the presence of that feature in the treatment?

Thank you in advance.

RvH

MicrobiomeData ALDEx2 • 1.8k views
ADD COMMENT
0
Entering edit mode

I am very impressed with your article. Like you said when you delete a result, run 3 it will be pushed from the left participant column to the right result column. I like it very much.

ADD REPLY
0
Entering edit mode

I value your insight and reaction. Would the advice still apply if I attempted to copy a picture and then paste it? You worked really hard to provide us with engaging the backrooms content.

ADD REPLY
0
Entering edit mode
Lucie • 0
@5e911037
Last seen 14 months ago
New Zealand

Hi,

I am no expert but I think you are looking for this webpage with ALDEX2 explained: https://www.bioconductor.org/packages/devel/bioc/vignettes/ALDEx2/inst/doc/ALDEx2_vignette.html

I understand it that you should use "effect" column not rab.win.*

ADD COMMENT

Login before adding your answer.

Traffic: 423 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6