Remove Unwanted Variation

[Ubaid_Midhat]

Dear admin,
I was wondering if RUVseq is available as a tool for use in galaxy instance. I could find it in GALAXY repositories but to install in GALAXY, I have to be an admin. Can you please let me know how to do this or if this is even possible.
Many thanks,
Midhat

[jennaj]

Welcome, @Ubaid_Midhat!

The tool is installed at the Galaxy EU server https://usegalaxy.eu.

Remove Unwanted Variation from RNA-seq data

I also made a request to add it to Galaxy Main https://usegalaxy.org, but that will need to go through a review/install process. Try it at Galaxy EU for now.

Thanks!

[Ubaid_Midhat]

Dear Jennifer,
Thank you for such a prompt response. I was able to use RUVseq on the EU galaxy server. While I get the normalized plots from the three methods, isn’t there a way to get normalized counts of genes using the different methods RUVseq uses. So far the output of RUVseq only had plots showing normalized datasets using different approaches and a tabular file that summarize the means from each method. I wanted the actual normalized counts for the datasets.

Can you please let me know how to achieve this?

Many thanks

Midhat

[jennaj]

@Ubaid_Midhat Odd - when I run tests with the tool at that server I end up with no output at all.

@hexylena It looks like a dependency is missing. I get green empty result datasets for all runs and the stderr has this at the end:

Loading required package: GenomeInfoDb
Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'GenomeInfoDbData'
Error: package 'GenomeInfoDb' could not be loaded

Test history (using test data/cases for tool): https://usegalaxy.eu/u/jenj/h/test-ruv

[vijay]

Hi,

I am using RUVseq it gave me the error below. I am using sailfish output files with the file names as " Sailfish_quant_C1_3.sf6.tab" with Gencode M25 annotation GTF file for mapping. Not sure if i am making any mistake. Your help is appreciated. Thanks in advance

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Atta"ching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: EDASeq
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

strsplit

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

anyMissing, rowMedians

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from ‘package:Biostrings’:

type

The following objects are masked from ‘package:base’:

aperm, apply

Loading required package: edgeR
Loading required package: limma

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

plotMA

Loading required package: ggplot2
reading in files with read.delim (install ‘readr’ package for speed up)
1 2 3 4 5 6
removing duplicated transcript rows from tx2gene
Error in $<-.data.frame(*tmp*, “TXNAME”, value = character(0)) :
replacement has 0 rows, data has 1869018
Calls: get_deseq_dataset → $<- → $<-.data.frame