Hello, I was looking for pearson correlation between a gene expression and the drug sensitivity dataset using the custom analyses tool. I am wondering how the q values are calculated because they are very small compared to the adjusted p-values I calculated myself using BH methods. Thank you so mu…

This thread provides links to the methodology / underlying methods - that might explain the difference you’re seeing: [image] Details on methodology of “Two Class Comparison” Feedback Would it be possible to include some details on the two class comparison custom analysis …

Thank you for your response! In the R script, the function p.adjust(method = ‘BH’) was used and I used the same function but I still can’t get the same p-value. And the link you suggested me is referring to two-class comparison tool, but I would like to know about the pearson correlation. Can I ha…

For the pearson correlations, we are using using R’s p.adjust(method=‘fdr’). According to the docs, that ‘fdr’ should be synonymous with ‘BH’, it should report the same q-value. However, looking at the UI, I don’t see a way to download the q-values, only the uncorrected p-values. (I imagine that wa…

Hello, I know the plot only shows uncorrected p-values, so I downloaded the whole table to get the q-values. However, when I use those uncorrected p-values in the downloaded table to calculated the q-value myself, the results are different compared to the q-values provided in the downloaded table. …

How are q-values for pearson correlation are calculated?

Q&A

dllahr December 20, 2022, 1:17am 2

This thread provides links to the methodology / underlying methods - that might explain the difference you’re seeing:

Topic		Replies	Views
P-values and q-values are identical for custom analysis of drug sensitivity AUC? Report an Issue	1	219	March 20, 2024
Repeated uniprot accesions and weird qvalues of proteomic data in the analysis tool Q&A portal , omics , data	1	213	March 20, 2024
Technical questions regarding the utilization of two-group comparison in custom analysis section Q&A	3	771	February 2, 2022
Breast cell lines, drug sensitivity Pearson correlation by gene Q&A	0	235	August 30, 2023
Details on methodology of “Two Class Comparison” Feedback	2	1242	August 19, 2024

How are q-values for pearson correlation are calculated?

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