Question: Why should the LD plot (LD heatmap) be created in control samples, not cases?
0
gravatar for sjunlee89
19 days ago by
sjunlee890
sjunlee890 wrote:

I would like to create the LD plot (LD heatmap) based on GWAS result.

On the other hand, I read that the LD plot should be made in control samples, not cases.

Is there any specific reason why the LD plot only comes from control samples?

Thanks advanced.

snp • 125 views
ADD COMMENTlink written 19 days ago by sjunlee890

On the other hand, I read that the LD plot should be made in control samples, not cases.

Please quote the source(s).

ADD REPLYlink written 19 days ago by Kevin Blighe35k

Thank you so much for your comment. Is there any specific reason why LD plot should be created in control samples?

ADD REPLYlink written 15 days ago by sjunlee890

I read that the LD plot should be made in control samples, not cases.

Where did you read this?

Is there any specific reason why LD plot should be created in control samples?

It depends on the analysis that you are doing.

ADD REPLYlink written 15 days ago by Kevin Blighe35k

I'm sorry to say that I am not familiar with GWAS analsys.

I read that the figures' descriptive in some of papers says "~~LD plots in ~~ controls".

I would like to know what you said that "it depends on the analysis that you are doing."

Thanks advanced.

ADD REPLYlink written 5 days ago by sjunlee890
1

Well, looking at LD in control samples and then comparing this to LD in samples with an inherited disorder/disease can reveal potentially useful information about the disease.

ADD REPLYlink written 5 days ago by Kevin Blighe35k

Thank you for your reply!

ADD REPLYlink written 5 days ago by sjunlee890
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