propr

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Question about significant proportionalities

3

Hello, @tpq! I write because I am having issues with the equivalency between traditional correlation's p-values and rho proportionality significance. One reviewer asked me for the p-values in my correlations...

alopgar

Question about how FDR is calculated

2

Hey I have a couple questions about the way FDR is calculated.... ## Using rho statistic The first involves rho: (see https://github.com/tpq/propr/blob/b85112e250eca9259b663fd6b0331d858eab3ea8/R/2-proprCall.R#L238 for the relevant line). For the FDR calculation...

mooreryan

Question about scaling propr to very large data sets (Part 2)

11

Hi all First of congrats on your wonderful software, just read about it and it looks very promising. I have a question/request. I have two datasets (coming from the same...

sapuizait

Hi, The recently added features to allow comparisons for more than 2 groups with post hoc tests are just great! However, pairwise comparisons are not always what we need. Instead,...

yanxianl

Question about lr2glm model.matrix argument

2

Hi there, I am working on sequence data from coral associated viral communities, which is in a dataframe of CLR transformed abundance data in which the columns are the samples...

MeggyC

Question about scaling propr to very large data sets (Part 1)

1

Hi Thom! Regarding the issue of large memory usage, I managed to reimplement what you proposed to me in the following pseudocode: ``` Alternatively, you could break down the whole...

suzannejin

Question about dimension reduction for single-cell and other data

3

As outlined in [A field guide for the compositional analysis of any-omics data](https://academic.oup.com/gigascience/article/8/9/giz107/5572529) CoDa should be the way to do single-cell RNA seq. I'd like to cluster cells (into cell-types)...

SilasK

Question about how to interpret rho and FDR

2

Hi @tpq, thank you for the wonderful CoDa methods you have implemented in propr! I read [Microbiome Datasets Are Compositional: And This Is Not Optional](https://www.frontiersin.org/articles/10.3389/fmicb.2017.02224/full) at the beginning of my...

taylorreiter

Question about why not to use negative rho

6

Hi! I have a quick question I couldn't entirely figure out of the documentation/vignettes. I created a propr object, as follows: ```r rho 0.9(, and adding all this features to...

maubarsom

Error in labRcpp(ncol(lr)) : negative length vectors are not allowed

14

Greetings. I'm experiencing what seems to be a size-dependent bug in `propr`. Here is a reproducible example ``` library(dplyr) library(propr) n.samples

grayfall