Question: p value and adjusted p value in microarray data analysis
0
gravatar for 7794karthi
5.8 years ago by
7794karthi0
7794karthi0 wrote:

i am doing microarray data analysis using R package. my doubt is regarding selection of DEG! whether i should 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??

 

R • 22k views
ADD COMMENTlink modified 3.8 years ago by hersiyuan620 • written 5.8 years ago by 7794karthi0

yes,I got all those p values and adjusted p values. But the problem is , all adjusted p values are greater than 0.3. so how should i choose DEG?

ADD REPLYlink written 5.8 years ago by 7794karthi0
2
gravatar for Sam
5.8 years ago by
Sam3.3k
New York
Sam3.3k wrote:

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 

ADD COMMENTlink written 5.8 years ago by Sam3.3k

If you use adjusted p-value, then you should use 0.05 or 0.01. However, if you use the un-adjusted p-value, you should use an adjusted threshold which should be 0.05/(number of tests). This is the bonferroni correction

ADD REPLYlink written 5.8 years ago by Sam3.3k

You can just use the add reply button instead of generating new results.

For any analysis you do, you should be able to get the p-value and the corresponding adjusted p-value. I am not sure what packages you use. But generally, you can just use the p.adjust function in R to get the adjusted p-value. You can use either the FDR or bonferroni correction

ADD REPLYlink written 5.8 years ago by Sam3.3k

yes,I got all those p values and adjusted p values. But the problem is , all adjusted p values are greater than 0.3. so how should i choose DEG?

ADD REPLYlink written 5.8 years ago by 7794karthi0

It means that after corrected for multiple testing, you have no significance. Sometimes, there just isn't any signficant finding /DEGs in the study. 

Or you can try to use FDR. If the multiple testing is based on Bonferroni, it will be more conserved and might therefore lead to very few findings

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Sam3.3k

than you sir..

ADD REPLYlink written 5.8 years ago by 7794karthi0
0
gravatar for andrew
5.8 years ago by
andrew510
United States
andrew510 wrote:

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.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by andrew510

Thank you sir.. i have understood the concept

 

ADD REPLYlink written 5.8 years ago by 7794karthi0

Sir, what is difference between adjusted p-value and p-value? which one is better to use?

ADD REPLYlink written 2.8 years ago by me.sr15100
0
gravatar for hersiyuan62
3.8 years ago by
hersiyuan620 wrote:

Think you.you help me.

ADD COMMENTlink written 3.8 years ago by hersiyuan620
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