User: annaA

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annaA10
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Posts by annaA

<prev • 29 results • page 1 of 3 • next >
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Comment: C: facet_wrap factor labbels
... structure(list(OTU = c("OTU019", "OTU019", "OTU019", "OTU019", "OTU019", "OTU019"), Sample = c("G15", "G117", "G131", "G119", "G128", "G118"), Abundance = c(0.2856728257715, 0.153067301965456, 0.137354461927612, 0.064094380216091, 0.0443080588357158, 0.043312727719327 ), group = structure(c(4 ...
written 6 weeks ago by annaA10
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(Closed) facet_wrap factor labbels
... Hello, I have the follwing code to generate a stack bar plot I have 3 variables I want to be present in the plot : species, sex ,sampling time I use facet_wrap to do it and not facet_grid because the 2 species have different amount of samples and the plot that facet_grid produces has empty space is ...
R ggplot2 plots written 6 weeks ago by annaA10 • updated 21 days ago by Biostar ♦♦ 20
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Comment: A: Perform two-way ANOSIM in R
... Hey I am working on some microbiome data and I am wondering the same is it possible to perform 2-way ANOSIM in R ., Thanks in advance A. ...
written 11 weeks ago by annaA10
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Comment: C: merge samples in phyloseq returns NAs
... yeah but do you see that some of the variables are changed for example the variable "primer" in the new object is translated to numeric values? I am using version 1.32.0 A ...
written 4 months ago by annaA10
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Comment: C: merge samples in phyloseq returns NAs
... In my data there are 3 samples with the same sample name( i.e "sample") FDR0033 lets say.So I thought if I merge them by "sample" it will work.But from what you are saying this is not correct. So I need to add a new variable "x" in which I will give the same name to these 3 samples only(?) and merge ...
written 4 months ago by annaA10
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Comment: C: merge samples in phyloseq returns NAs
... Sure ! next time I'll do it right ...
written 4 months ago by annaA10
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Comment: A: merge samples in phyloseq returns NAs
... Hey thanks for your reply . So the output of the str(sample_data(f_data)) is the following 'data.frame': 237 obs. of 15 variables: Formal class 'sample_data' [package "phyloseq"] with 4 slots ..@ .Data :List of 15 .. ..$ : chr "G1" "G10" "G100" "G101" ... .. ..$ : ...
written 4 months ago by annaA10
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merge samples in phyloseq returns NAs
... Hello I am working in a dataset which contains several categorical variables in the meta data (sample_data). i want to merge some replicates and maybe in the next steps I will need to merge other samples to. To do so I am using the merge_samples function as follows f_data: original phyloseq object ...
R biom phyloseq written 4 months ago by annaA10
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filter OTU table based on absolute abundance
... Hello, Currently I am working with 16S rRNA - metabarcoding data. I have a question about filtering the OTU table prior to downstream analysis. From my reading I am not sure if I should filter the OTU table based on absolute abundance or relative abundance. I know its super basic question, but it ...
metabarcoding microbiome otu written 4 months ago by annaA10 • updated 4 months ago by antonioggsousa1.5k
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Comment: C: erros in dowloading SRA data
... Thanks for the recommendation I will check it right away! ...
written 5 months ago by annaA10

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For TPM or FPKM for single cell RNA seq experiment ?

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