I have been conducting pathway analysis on my RNA-seq data using the Deseq2/GAGE workflow. I ran GAGE and it worked well generating a list of affected pathways. I used “KO” annotations from kegg.gsets (species=”ko”) as I am working on a non-model organism. I am now trying to extract data for essential member genes in my perturbed pathways with essGene() However, I keep getting the error message “Error in expdata[rownames(b)[sel], ] : incorrect number of dimensions”. Is this possibly because my input data is not a column for each sample as demonstrated for microarray data in the 2009 GAGE vignette but a vector of 1 set of pairwise log2fold changes generated by Deseq2? How can I resolve this issue? Any advice would be much appreciated, thanks.
Format of my data “deseq2.fc”- a vector with KO gene IDs as names and pairwise log2fold expression values:
Named num [1:5638] -0.0456 -0.2300 0.4829 -0.6356 0.6871 ...
- attr(*, "names")= chr [1:5638] "K03598" "K12035" "K03556" "K16740"….
The code I used:
gageres <- gage(deseq2.fc, gsets= kegg.ko, ref=NULL, samp=NULL)
chr [1:1176] "K00234" "K00235" "K00236" "K00237" ...
# Everything seems to work up until this point below:
essData=essGene(gs, deseq2.fc, ref=NULL, samp=NULL)
Error in expdata[rownames(b)[sel], ] : incorrect number of dimensions
1: essGene(gs, deseq2.fc, ref = NULL, samp = NULL)