Background setting

[matwgmkw]

Hi. I am wondering what is the "background" setting? Is it the total number of genes in the genome? Thanks.

[anfederico]

Hi, yes that is correct.

[tetomonti]

To add to that, the background depends on the assay.

E.g., if you use an Affymetrix microarray that measures 13,000 features, then 13,000 is the background.

If you use a protein array such as SomaScan measuring, say, 3,500 proteins, then 3,500 is the background.

If you use RNAseq, than yes, the background is the number of transcripts in the transcriptome (i.e., the number of transcripts RNAseq can conceivably detect).

—ste

On Aug 3, 2020, at 4:17 PM, anfederico notifications@github.com wrote:

Hi, yes that is correct.

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[matwgmkw]

To add to that, the background depends on the assay. E.g., if you use an Affymetrix microarray that measures 13,000 features, then 13,000 is the background. If you use a protein array such as SomaScan measuring, say, 3,500 proteins, then 3,500 is the background. If you use RNAseq, than yes, the background is the number of transcripts in the transcriptome (i.e., the number of transcripts RNAseq can conceivably detect). —ste … On Aug 3, 2020, at 4:17 PM, anfederico @.***> wrote: Hi, yes that is correct. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACIAGH7VCIQHLLSYZ5XJQQLR64LOLANCNFSM4OVFCTFA.

I see. Thank you.

[anfederico]

I will leave this issue open for a bit as this is a FAQ.

[tilofrei]

As a reference broad's msigdb sets the background to 40786 for their online tool: