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Gene set variation analysis
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The data type of exprData matrix: for ssgseaParam, integer counts? Continuous expression data? #171

Closed jnhv closed 5 months ago

jnhv commented 5 months ago

Dear Developer,

Thank you for your outstanding work – it's been incredibly helpful!

Quick question: What's the ideal input for ssgseaParam—continuous expression data (e.g., log-scale microarray, RNA-seq log-CPMs/RPKMs/TPMs) or integer counts from RNA-seq? Additionally, I noticed that when using gsvaParam, users have the flexibility to adjust parameters like kcdf. However, it appears that this level of customization is not offered within ssgseaParam.

Could you shed some light on this discrepancy or perhaps guide me towards any alternative means to achieve similar functionality within the context of ssgseaParam?

Thank you once again for your dedication and for considering my request.

Best regards, Jin

rcastelo commented 5 months ago

Hi, thanks for using GSVA!

The ssgseaParam() constructor function serves the purpose of building a parameter object to use the ssGSEA method first published by Barbie et al. (2009, see Online Methods, subsection 'Signature projection method'), which is not a method we developed, we only provide an efficient implementation of this method in R and Bioconductor. I'd say probably ssGSEA works best with normalized logCPM or logTPM units of expression, but you may get a more authorative answer in the official support site for ssGSEA, which I believe is this Google Group.

Regarding the question about why the ssgseaParam() function has different arguments than the gsvaParam() function, the reason is that these function build parameter objects for different methods, i.e., the GSVA method is different from the ssGSEA method. You may find this discussed in the GSVA paper.

cheers,

robert.

jnhv commented 5 months ago

Hi, thanks for using GSVA!

The ssgseaParam() constructor function serves the purpose of building a parameter object to use the ssGSEA method first published by Barbie et al. (2009, see Online Methods, subsection 'Signature projection method'), which is not a method we developed, we only provide an efficient implementation of this method in R and Bioconductor. I'd say probably ssGSEA works best with normalized logCPM or logTPM units of expression, but you may get a more authorative answer in the official support site for ssGSEA, which I believe is this Google Group.

Regarding the question about why the ssgseaParam() function has different arguments than the gsvaParam() function, the reason is that these function build parameter objects for different methods, i.e., the GSVA method is different from the ssGSEA method. You may find this discussed in the GSVA paper.

cheers,

robert.

thank you！！！