Hello everyone
Regarding the package singscore, in particular the function simpleScore, that allows to score a gene expression dataset based on one or two gene sets, I was wondering if the signature scores from different gene sets are comparable.
Say I have 4 gene sets that I use to classify tumor samples to molecular subtypes, my idea is to score the gene expression dataset with each one of the 4 gene sets separately, and then compare the signature scores across the 4 gene sets for each sample.
I would like to know if the scores are comparable in absolute terms.
Here an example output (note that I run each gene set separately and then merged the results)
id Gene_set_1 Gene_set_2 Gene_set_3 Gene_set_4
sample_1 -0.0625 -0.194 0.298 0.182
sample_2 -0.0706 -0.211 0.273 0.218
sample_3 0.0366 -0.204 0.183 0.263
sample_4 -0.0219 -0.221 0.325 0.215
sample_5 -0.0215 -0.232 0.267 0.2
sample_6 -0.00629 -0.186 0.205 0.255
sample_7 -0.0425 -0.202 0.177 0.217
sample_8 -0.0985 -0.219 0.252 0.191
sample_9 -0.0726 -0.194 0.272 0.154
sample_10 -0.0513 -0.226 0.245 0.161
Can I say for example that for sample_1 the gene sets scores ranked are: Gene_set_3 > Gene_set_4 > Gene_set_1 > Gene_set_2 ?
Thanks
PS: cross-posted to bioconductor
can i know the procedure to perform singscore for a microarray dataset(affymetrix) and other signatures (gene-sets) . can anyone help with script