Question: Identifying differentially expressed genes from Wild type and Knockout data
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gravatar for Muhammad Haseeb
2.9 years ago by
Ajou University, Suwon, South Korea
Muhammad Haseeb50 wrote:

Dear Researcher,

I am analyzing the microarray data of mouse_402 by using Affymetrix console Expression and normalized through RMA.We have total 8 chip, 4 Wild type (WT day 4 (r1),WT day 4 (r2),WT day 6 (r1), WT day 6 (r2)) and 4 Knockout similarly (KO day 4 (r1)...........). After generating the annotation file and log2 value calculation the final Excel file structure are as follows.

Probe_ID Gene_name Average WT day 6 Ave KO d6 Day 6 log2 Ave WT d4 Ave_KO_d4 Day 4 log2

xx-at ABC 29.3 32.5 0.17 31.2 29.5 -0.11

xx-at XYZ 1338 1500 -0.14 387.9 400 0.3

Now, I want to identify the differentially expressed genes. How we calculate T-Test and fold value and which 2 columns need to select for T-Test. I am working in Excel. Is there any good free software to import the excel file and calculate the DEG? I will be highly obliged. Thank you

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Muhammad Haseeb50

Hello!

You should have a look to limma (https://bioconductor.org/packages/release/bioc/html/limma.html). The usersguide.pdf is quite dense but should provide all the informations you need to perform and understand such type of analysis. NB: This solution won't work with excel.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by VHahaut1.1k
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