Post by Subhashini D on Jul 26, 2021 6:16:18 GMT -5
After performing FA clustering for the DEGs (Input gene list), there appears a result table.
1. In the table, how the Fold Enrichment, Bonferroni values, Benjamini values and FDR are calculated by DAVID ? Though understood that Fold enrichment is the enrichment of DEGs wrt background population genes and Benjamini values comes from Modified Fisher Exact p values, how every values are calculated ?
2. How to interpret these values ? When the result window appears, the table shows p values and Benjamini values. While downloading the result table, it has all the 5 values - p values, Fold enrichment, Bonferroni, Benjamini and FDR. How to understand these values wrt to the annotated term ?
I tried to understand, How these values arrive thro' the reference papers quoted by DAVID.
A) Šidák, Z. (1967). "Rectangular Confidence Regions for the Means of Multivariate Normal Distributions." Journal of the American Statistical Association 62:626-633.
B) Benjamini, Y. and Hochberg, Y. (1995). "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing." Journal of the Royal Statistical Society. Series B, Statistical Methodology 57:289-300.
C) Benjamini, Y., and Hochberg, Y. (2000). "On the Adaptive Control of the False Discovery Rate in Multiple Testing with Independent Statistics." Journal of Educational and Behavioral Statistics 25:60-83.
But, it's tough to understand the logic behind these papers.
Please, Can someone explain of how to interpret the result with these values ?
Regards,
Subhashini D
1. In the table, how the Fold Enrichment, Bonferroni values, Benjamini values and FDR are calculated by DAVID ? Though understood that Fold enrichment is the enrichment of DEGs wrt background population genes and Benjamini values comes from Modified Fisher Exact p values, how every values are calculated ?
2. How to interpret these values ? When the result window appears, the table shows p values and Benjamini values. While downloading the result table, it has all the 5 values - p values, Fold enrichment, Bonferroni, Benjamini and FDR. How to understand these values wrt to the annotated term ?
I tried to understand, How these values arrive thro' the reference papers quoted by DAVID.
A) Šidák, Z. (1967). "Rectangular Confidence Regions for the Means of Multivariate Normal Distributions." Journal of the American Statistical Association 62:626-633.
B) Benjamini, Y. and Hochberg, Y. (1995). "Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing." Journal of the Royal Statistical Society. Series B, Statistical Methodology 57:289-300.
C) Benjamini, Y., and Hochberg, Y. (2000). "On the Adaptive Control of the False Discovery Rate in Multiple Testing with Independent Statistics." Journal of Educational and Behavioral Statistics 25:60-83.
But, it's tough to understand the logic behind these papers.
Please, Can someone explain of how to interpret the result with these values ?
Regards,
Subhashini D