Marwa

percent and counts on two different lines?

1

Hey I am using ps_venn which is using eulerr underneath. In the case of using percent and counts, any way to separate them on two different lines so I don't...

Error in quantile.default(abs(mat), 0.975) : missing values and NaN's not allowed if 'na.rm' is false?

5

I am not sure why I am getting this error Could you please help me with any info so that I could move forward?  I attached the ps.prev0 here:...

plot_cladogram()

5

good morning :) how to solve the issue of the overlapping of the labels in the cladogram? I can't find any option to change the place of the label on...

prevalence method figure; Prevalence (Negative Controls) on x-axis against Prevalence (True Samples) on y-axis?

1

hello .. I went for the prevalence method; my plot using this command is different from the one in the tutorial (having just few as you can in the below-attached...

transform phyloseq object to a list?

1

Could you please let me know how to transform my phyloseq object to be accepted as input data to use ggVennDiagram? Many thanks M

alpha diversity comparison between rarified and unrarified?

1

Hello I am trying to to make a comparison (at level of alpha diversities) between the rarified (ps.rare) versus the unrarified (ps.prev) phyloseq object as follows: > ps.prev phyloseq-class experiment-level...

compare_means() and pairwise_wilcox_test() different results?

1

Hello amazing guys Now I found there is a difference that I can't grasp between compare_means() and pairwise_wilcox_test() looking in to stat difference between intes.dsChall**MMV** and intes.dsChall**VMV** my codes ```...

compare_means() & wilcox_test() gave different stat significance results, why?

1

Hi @kassambara As a response to your kind replies on different issues. I used compare_means() and wilcox_test() to find out that both gave different results (statistical significance) kindly find the...

Could you please advise how to make comparisons between both treatments (marine and vegetable) for each Genus? here is my code and figure ``` # Box plot facetted by "treatment"...

pathway analysis on FDR?

1

HI guys It is not an issue it a question regarding enrichmenet analysis. Do you recommend running pathway analysis without FDR cutt-off so it is independent of DGE genes? I...