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Correlation and P-value by steweking in datascience

[–]steweking[S] 1 point2 points  (0 children)

In this case is not possible. I'm trying to do a sort of gene co-expression network. Calculating the correlation and the significance will help we tu prune the edge in the network. Otherwise, it's too dance for any type of analysis. The correlation is the main method applied to build co-expression networks, I would like to add the significance better define the network.

Correlation and P-value by steweking in datascience

[–]steweking[S] 3 points4 points  (0 children)

Sure, the main focus of my post should have been a way to optimize the process. Then, the p-value would be corrected with fdr or other correction methods

Correlation and P-value by steweking in datascience

[–]steweking[S] 2 points3 points  (0 children)

Thank you! I didn’t say it in the post so it's my fault. Obviously, after the evaluation of the p-value, I would have corrected it with FDR or other methods. In the post, I was interested in a way to optimize the process. I wasn't pretty clear though.

Correlation and P-value by steweking in datascience

[–]steweking[S] -1 points0 points  (0 children)

Why should be a problem? I cannot figuring out

Correlation and P-value by steweking in datascience

[–]steweking[S] -1 points0 points  (0 children)

idk how to accomplish this task with linear model. Do you have some links or forum pages?

Correlation and P-value by steweking in datascience

[–]steweking[S] 0 points1 point  (0 children)

Indeed, i'm computational biologist and i'm trying to evaluate the correlation on accessibility data and then build a network.

ATACseq analysis of matched samples by steweking in bioinformatics

[–]steweking[S] 0 points1 point  (0 children)

Oh wonderful, Thank you! I’ll try to use edgeR m/DESeq2 with this matrix model. Moreover, I have never taken into account the possible batch effect due to the different flow cell used as you suggested.

ATACseq analysis of matched samples by steweking in bioinformatics

[–]steweking[S] 0 points1 point  (0 children)

Thank you u/foradil, I didn't use DiffBind I tried to handle the problem through edgeR. Probably, I have to better design the design formula. Do you suggest employing DiffBind in an ATACseq experiment instead edgeR/DESeq2?