p value and adjusted p value in microarray data analysis

Question

[7794karthi]

I am doing microarray data analysis using R package. My doubt is regarding selection of DEG. Should I consider p VALUE < 0.05 or ADJUSTED p VALUE < 0.05 for selection of DEG? I get adj p values >0.3. What should I do now? On what basis the threshold of p value or adj p value should be set?

[hersiyuan62]

Thank you. You helped me.

Answer 1

[Sam]

You should use the adjusted p-value to account for multiple testing. You should also know what kind of adjustment was done, be it FDR or bonferroni. There is no absolute "best" p-value threshold, we usually just use 0.05 or 0.01 as a common practice

Answer 2

[andrew]

As Sam mentioned, if your smallest p-value is 0.3, then it means you do not have any significant DE genes. Did you perform any QC or normalization before calculating differential expression?

In our application, iPathwayGuide, we recommend DEG selection be based on adjusted p-value (and log2FC). Our default thresholds for DEG selection are Adj.pv < 0.05 and absolute value log2FC > 0.6.

If there are no DEGs, then it means you might need to re-run some of your experiments or that the two phenotypes are not dissimilar.

I hope this helps.

[7794karthi]

Thank you sir.. I have understood the concept

[me.sr1510]

Sir,

What is the difference between adjusted p-value and p-value? Which one is better to use?