Question: Best way of presenting "absolute" expression values (edgeR)
gravatar for Sindre Lee
4.3 years ago by
Sindre Lee100
Sindre Lee100 wrote:
Hi! We want to classify a new type of glands by ranking genes by expression level using RNAseq. We don't have any good controls, so we just want to see a ranked list of genes. I have used Cufflinks RPKM values, but if I want to use edgeR, is this a valid way of doing it using featureCounts: fc <- featureCounts(files=targets$Targets,nthreads=8, isGTFAnnotationFile=TRUE, GTF.attrType="gene_id", GTF.featureType="exon", useMetaFeatures=TRUE, annot.ext="genes.gtf") x <- DGEList(counts=fc$counts, genes=fc$annotation) expr <- calcNormFactors(x) expr_norm <- rpkm(expr, log=FALSE,gene.length=x$genes$Length) # Getting gene length from FeatureCounts, using rkpm() in the edgeR package, not Rsubread.. Then just write out this table.. Thanks!
ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Sindre Lee100
Hi! I know a lot of people do the following: 1. Take a list of differentially expressed genes 2. Fetch the FASTA files for protein coding genes 3. Predict if secretory by using SignalP My question is, does it exist a list/database of known/predicted secretory protein coding genes from hg19? That would be much more efficient than many people predicting the same proteins a lot of times..
ADD REPLYlink written 4.3 years ago by Sindre Lee100
gravatar for Gordon Smyth
4.3 years ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:

Yes, your code is fine for getting normalized RPKM from featureCounts and edgeR.

Your code is similar to the public case study:

In the latest version of edgeR, you can even simplify the code to

expr_norm <- rpkm(expr)


ADD COMMENTlink modified 14 months ago • written 4.3 years ago by Gordon Smyth34k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 127 users visited in the last hour