Selection LogFC when collapsing with Abs max

[최성수]

Hi,

I'm trying to Collapse with my data

I selected 'Abs_max_of_probes', but my data has same LogFC Abs value

like, '-0.0888/0.0888', '-0.271, 0.271'... 

GSEA software selected positive values everytime, but I couldn't find the description about this.

Could you tell me the logic about this? and why only positive values were selected.

thank you.

[Anthony Castanza]

Hello,

Our official stance is that anything that results in tied values is a condition that we don't support or advise.

Unofficially, I suspect that what is happening here is that when parsing the ranked list in ABS_MAX mode the list is still indexed in descending order from largest to smallest (most negative)

so if you have

Gene_A_1 200

Gene_A_2 100

Gene_A_3 -200

the genes have index 1, 2, 3

So when doing abs_max, I think what is probably happening is that it is testing (abs(Gene_A_1), index 1) against (abs(Gene_A_3), index 3) the first part is tieing so it is then resolved by the index where the "first" index is being selected, which will cause the earliest positive occurrence of the tied mapping to be picked.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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