Are singscore scores comparable between gene sets?
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2.3 years ago
Pietro ▴ 110

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 ?


PS: cross-posted to bioconductor

singscore GSVA GSEA subtypes genesets • 874 views
Entering edit mode

can i know the procedure to perform singscore for a microarray dataset(affymetrix) and other signatures (gene-sets) . can anyone help with script


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