Question: QIIME Differential abundance on multiple studies
0
gravatar for syafiqkamarulazman
2.2 years ago by
syafiqkamarulazman0 wrote:

I have a collection samples spanning 3 different studies. I am performing differential abundance to identify the OTUs which are significant in seawater vs membranes.

With the entire collection, I can easily do

differential_abundance.py studies.biom -o diff_otus.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceType \
                                       -x Membrane -y Seawater -d

 

I also want to perform differential abundance for each study individually.

Can I just add a new column into my mapping file called SourceStudy to discriminate the study and the source type at the same time?

Will the results from DESeq2 from running the following be meaningful?

differential_abundance.py studies.biom -o diff_otus_s1.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceStudy \
                                       -x S1Membrane -y S1Seawater -d
differential_abundance.py studies.biom -o diff_otus_s2.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceStudy \
                                       -x S2Membrane -y S2Seawater -d
differential_abundance.py studies.biom -o diff_otus_s3.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceStudy \
                                       -x S3Membrane -y S3Seawater -d

 

Should I instead split the BIOM table into individual studies and then perform differential abundance like the following?

differential_abundance.py study1.biom -o diff_otus_s1.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceType \
                                       -x Membrane -y Seawater -d
differential_abundance.py study2.biom -o diff_otus_s2.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceType \
                                       -x Membrane -y Seawater -d
differential_abundance.py study3.biom -o diff_otus_s3.txt -a DESeq2_nbinom \
                                       -m source_type.map -c SourceType \
                                       -x Membrane -y Seawater -d
deseq2 qiime • 369 views
ADD COMMENTlink modified 2.2 years ago by Michael Love26k • written 2.2 years ago by syafiqkamarulazman0
Answer: QIIME Differential abundance on multiple studies
1
gravatar for Michael Love
2.2 years ago by
Michael Love26k
United States
Michael Love26k wrote:

You’ll have to ask the authors of the differential_abundance.py script. I didn’t write it.

ADD COMMENTlink written 2.2 years ago by Michael Love26k

Thanks for letting me know, I should have tried the QIIME forums first. Thanks anyway
 

ADD REPLYlink written 2.2 years ago by syafiqkamarulazman0
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