microarray DEG analysis

Question

[bioinformatics]

Hi,

I was following this microarray bioinformatic differential gene expression analyses tutorial R code: https://github.com/Lindseynicer/How-to-analyze-GEO-microarray-data/blob/main/GSE_analysis_microarray.Rmd

I analysed GSE30929 instead.

However, when I run this line of code
fit2 <- contrasts.fit(fit, contrasts)
fit2 <- eBayes(fit2)

topTable(fit2)
topTable1 <- topTable(fit2, coef=1)
topTable2 <- topTable(fit2, coef=2)
topTable3 <- topTable(fit2, coef=3)
topTable4 <- topTable(fit2, coef=4) 

I only get a DE table of some of the probes.

I was wondering how I might create a table with all the genes/probes and export it as a csv/txt file? Do you know how to do this?

Also include the annotations/gene names in the table Thankyou

Answer 1

[ATpoint]

That is why it is recommended to consult the manual of the tools you use (limma, a Bioconductor package) and read the function help (here ?topTable). Please do ?topTable and go through the option, I'm sure you will find the answer, which is a great learning experience.

[bioinformatics]

Also, do you know why the DEG results in this r code are different every time?

[ATpoint]

limma itself is deterministic, measning same results in each run, given that input data, code and software versions are the same. If results change then because of any custom code. For more details you would need to add a reproducible example.