Question: Using PEER to identify hidden confounders in RNA-seq data (not working)
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gravatar for rodrigo.duarte88
8 months ago by
rodrigo.duarte8820 wrote:

Hi all,

I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio/peer/wiki/Tutorial ), but without much luck, and there's not much help available unfortunately. Anyone used this tool before and could advise?

I have installed R-PEER on Conda, but am having issues with following with the PEER pipeline, to identify 10 hidden confounders in my expression data. I was wondering if anyone could advise? I couldn't find much help online.

> $ source activate r-peer (r-peer) 
> $ R  
>library(peer) 
> expr <- read.table("~/raw_counts.tsv", header=TRUE)
> dim(expr) 
>[1] 14211   538      # 14211 row-genes, 538 col-samples 
> expr <- t(expr)    # transpose 
> model = PEER()
> PEER_setPhenoMean(model,as.matrix(expr))
> [1] NA                      # in the tutorial, it says this should be "NULL" 
> PEER_setNk(model,10)  # so PEER identifies 10 hidden confounders 
>PEER_getNk(model) [1] 10
> PEER_update(model)
>         iteration 0/1000
>         iteration 1/1000 
>Converged (bound) after 1 iterations NULL     ###### why isn't it iterating?
> 
> 
> sessionInfo() R version 3.4.1 (2017-06-30) Platform:
> x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS
> 
> Matrix products: default BLAS:
> /home/rodrigo/miniconda2/envs/r-peer/lib/R/lib/libRblas.so LAPACK:
> /home/rodrigo/miniconda2/envs/r-peer/lib/R/lib/libRlapack.so
> 
> locale:  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C          
> LC_TIME=C.UTF-8  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
> LC_MESSAGES=C.UTF-8  [7] LC_PAPER=C.UTF-8       LC_NAME=C             
> LC_ADDRESS=C [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8
> LC_IDENTIFICATION=C
> 
> attached base packages: [1] stats     graphics  grDevices utils    
> datasets  methods   base
> 
> other attached packages: [1] peer_1.0
> 
> loaded via a namespace (and not attached): [1] compiler_3.4.1
ADD COMMENTlink modified 8 months ago by Martin Morgan ♦♦ 23k • written 8 months ago by rodrigo.duarte8820

PEER isn't a Bioconductor package so you'll have more luck directing questions to the maintainer or other resource identified in packageDescription("PEER")

ADD REPLYlink written 8 months ago by Martin Morgan ♦♦ 23k

Oops, sorry about that! To be fair, I think am going to try "sva", looks like there's more documentation for that one. Thanks, Martin!

ADD REPLYlink written 8 months ago by rodrigo.duarte8820
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