Off topic:goseq pwf length bias plot: help interpreting plot
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6.1 years ago

Hi! I am using goseq on some bovine data and I am using Ensembl IDs for bovine genome UMD3.1, which is not supported by goseq, so I had to input lenght and GO information manually. I tried obtaining length information 2 ways: 1) from featCounts files results; 2) from biomaRt.

Both gave me weirdly shaped plots. Not sure if I'm doing something wrong. The graphs are in totally opposite direction then I expected them to be ( instead of going up and stabilizing as I expected, they are going down).

Below are the codes of how I obtained length info and plots, as well as the plots

1) Using featureCounts results:

featCountsData <- read.table("charolais_145A_TGACCA.featCounts.txt", header=TRUE, comment.char = "#", sep="\t")

featCountsLengthData <- as.numeric(featCountsData[,"Length"])
names(featCountsLengthData) <- featCountsData$Geneid

LenData <- names(geneLengthData) %in% names(genes)
LenData <- geneLengthData[LenData]

pwf <- nullp(DEgenes = genes, = LenData, = TRUE)

2) Using Biomart:

txsData <- makeTxDbFromBiomart(biomart ="ensembl", dataset = "btaurus_gene_ensembl")
txsByGene <- transcriptsBy(txsData,"gene")
geneLengthData <- median(width(txsByGene))

BiomartLenData <- names(geneLengthData) %in% names(genes)
BiomartLenData <- geneLengthData[testLenData]

pwf <- nullp(DEgenes = genes, = BiomartLenData, = TRUE)

PLOT 1: Length info obtained from featureCounts:

PLOT 2: Length info obtained from biomaRt

Any help is appreciated!

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