Question: Create your own gene set collection
0
gravatar for celia.escher
13 days ago by
celia.escher0 wrote:

I am interested in analyzing the enrichment of immune cell types in my RNA-seq data (human bulk biopsy samples) by using gene set variation analysis (GVSA). However, I am pretty lost with GSVA and GSEABase packages for R and do not know the structure of files that need to be prepared for GVSA (e.g. the gene set collection object).

I would like to use some pre-defined gene sets that identify immune cells which I retrieved from table S1A here: https://clincancerres.aacrjournals.org/content/suppl/2018/04/17/1078-0432.CCR-17-3509.DC1 to follow the GSVA molecular signature identification guide (4.1 in the GSVA guide here: https://www.bioconductor.org/packages/release/bioc/vignettes/GSVA/inst/doc/GSVA.pdf)

Could you give me a clue on how to prepare this gene set collection???

Thank you so much in advance!!!

rna-seq R • 97 views
ADD COMMENTlink modified 11 days ago • written 13 days ago by celia.escher0
1
gravatar for igor
13 days ago by
igor9.8k
United States
igor9.8k wrote:

For GSVA, gene sets can be provided either as a list object or as a GeneSetCollection object. It's easier to use a list. Each component is a gene set. The name is the name of the gene set and the value is a vector of genes. For example:

my_gene_sets <- list(gene_set_1 = c("geneA", "geneB", "geneC"))
ADD COMMENTlink modified 13 days ago • written 13 days ago by igor9.8k
0
gravatar for celia.escher
11 days ago by
celia.escher0 wrote:

Thank you so much, Igor!!! I also found how to import the gene list here: https://stackoverflow.com/questions/6602881/text-file-to-list-in-r

Now I do not know how to solve this other problem when using GSVA...

GSVA_ES <- gsva(ExprSet, GeneSetCol, mx.diff=FALSE, verbose=FALSE, parallel.sz=1)

Error in (function (classes, fdef, mtable): unable to find an inherited method for function ‘gsva’ for signature ‘"data.frame", "list"’

Could it be due to the input files? The expression set is a data frame that contains genes (rows) and samples (columns) in log2 of normalized counts from RNA-seq. I have fixed this file so gene names will be only displayed as row names and not as an additional variable (column 1 for example).

Thank you!!!

ADD COMMENTlink written 11 days ago by celia.escher0
1

The expression set should be a matrix.

ADD REPLYlink written 11 days ago by igor9.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1080 users visited in the last hour