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Significantly changed genes increase after Benjamini Hochberg correction

Hello, I am trying to analyze a big dataset via student t-test. Data set includes two different data sets coded as GSE18489 and GSE31068 (they can be used together as authors told me). When I use ttest2 function of Matlab, I have about 5200 significantly changed genes. When I use Benjamini Hochberg correction via mafdr command, I have about 5600 significantly changed genes.

What can be the main reason of this result?

Thank you.

microarray matlab ttest fdr
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written by hkarakurt hkarakurt

Seems a bit suspicious... are you looking at the results in Excel, Excel for Mac, or Open/Libre Office? Either of these may have distorted the results. Also, if you're in a 'Latin' nation, including Italy, Spain, Portugal, all of Latin America and Central America, and some African nations, then a comma will be the decimal specifier and not a dot.

If you're using R, be sure also that scientific notation is not causing an issue by setting options(scipen=999) just before you generate P values. This sets decimal places to 999.

Also specify the exact command that you use when correcting for P values.

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written by Kevin Blighe Kevin Blighe

Without seeing the p-values and knowing what you've done, it's hard to say precisely.

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written by Jean-Karim Heriche Jean-Karim Heriche

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