Design and contrasts for tidybulk test differential abundance function about tidybulk HOT 9 CLOSED

you are missing a c() for the first command.

Please try and let me know. Also this command depend on the column names of your dataset (similarly to model.matrix command)

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Is the reply here helpful?

https://support.bioconductor.org/p/9149049/#9149050

otherwise I can elaborate further.

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Thank you. Useful comment.

Will this work?

test_differential_abundance( ~treatment, method = “”, contrast = (“treatmentT1 + treatmentT2 + treatmentT3)/3 - treatmentControls")
will work for edgeR and limma-voom right.

will
test_differential_abundance (~treatment, method = “DESeq2”, contrast = list (c(“ treatmentT1 + treatmentT2 + treatmentT3)/3 - treatmentControls”)
work for DESeq2
Am I right?

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Got it . Thank you. I will try this first thing tomorrow and let you if this works. I will also ensure the column names are ok & matching the ones specified in the function.

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I tried the following code
counts %>% test_differential_abundance( ~ , method = “DESeq2”, contrasts = list (c(-1, 1/3, 1/3, 1/3)), omit_contrast_in_colnames = TRUE)

No errors while running the DESeq2 codeBut when I check number of DE genes , I get 43 Up and 15100 odd genes Downregulated. That seems odd. Right?

I used the following for edgeR/ limma voom
counts %>% test_differential_abundance( ~ , method = “”, contrasts = c(-1, 1/3, 1/3, 1/3), omit_contrast_in_colnames = TRUE)

I get the following warnings while running edgeR/voom

Are there issues related to default edgeR in tidybulk? https://support.bioconductor.org/p/9147697/

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Update for the DESeq2. I tried excluding the intercept in the formula by specifying ~ 0 + treatment . That seem to work! Yet to figure something out for edgeR/voom

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I used the following for edgeR/ limma voom counts %>% test_differential_abundance( ~ , method = “”, contrasts = c(-1, 1/3, 1/3, 1/3), omit_contrast_in_colnames = TRUE)

couple of points,

• always specify a method, not "".
• Please see documentation ?test_differential_abundance on how to set contrasts for edgeR and voom. Please execute the examples in the documentation first.

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Thank you. I am working on a different computer. so I am manually typing the commands and the output here. It’s difficult to type the entire method , so I obviously change the method argument and take care of the syntax when I try the command on my work PC.
The above command for edgeR/limma generated the warnings as shown in the picture above. Anyways thank you for the help.

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