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biocore / songbird

Vanilla regression methods for microbiome differential abundance analysis
BSD 3-Clause "New" or "Revised" License
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collapsing at taxa level and then use in songbird pipeline is right way or not? #164

Closed princy149 closed 1 year ago

princy149 commented 2 years ago

hi @mortonjt, here I have a quick question that regarding using of songbird pipeline for my input if I want to collapse at taxa level (like phylum or genus) and then use my taxa_coolapse_biom file in songbird pipeline, then it is right way or not? is there any effect on the differentially abundance results if i use collapse_taxa_biom?

looking for your suggestion, Thank you,

mortonjt commented 2 years ago

Collapsing is fine

On Wed, Jun 1, 2022 at 5:15 PM UPASNA SRIVASTAVA @.***> wrote:

hi @mortonjt https://github.com/mortonjt, here I have a quick question that regarding using of songbird pipeline for my input if I want to collapse at taxa level (like phylum or genus) and then use my taxa_coolapse_biom file in songbird pipeline, then it is right way or not? is there any effect on the differentially abundance results if i use collapse_taxa_biom?

looking for your suggestion, Thank you,

— Reply to this email directly, view it on GitHub https://github.com/biocore/songbird/issues/164, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXO5YBUHUGUUNMSVNNLVM7HFLANCNFSM5XSYTBGQ . You are receiving this because you were mentioned.Message ID: @.***>

princy149 commented 2 years ago

Thank you very much for so quick response :)