What object in GEO2R R code environment to use for ggplot2 Volcano and listing DEG?

Question

[qmarulfiz]

Hi,

I copy the R script from GEO2R into my RStudios.

I want to create a table in R that contain Different Expressed Gene list that show Gene Entrez ID, Log2 Fold Change, adjusted p-value and P-value.

The object that I call to display these information still contain multiple Gene ID and Gene.Symbol in one row mapped to one array probe (i think). Some probes does not even have Gene.ID and Gene.Symbol. Example Column as below.

1. Gene ID: 102640145///102631971///100039019, 20860
2. Gene Symbol: Gm21286///LOC102631971///Mup-ps12, Sult1e1

(I want the table to display gene like Sult1e1 which only have 1 id and 1 symbol, but gene Gm21286 have multiple ID and symbol in them)

Now I was wondering which object should I call in using GEO2R script to display gene list and other information that is useful for plotting without having seeing above example.

Alternatively can someone point to me if I do wrong here. Should I filter the list from multiple Gene.ID and empty row first? How to seperate gene with multiple info in it? Or am I just dumb like trying to do things in long way, because there is much simpler way such as using other bioconductor packages etc...

[badribio]

Looks like you are trying to analyze array data, for each gene you will have multiple probes and that is what you see when you say "multiple gene ID" read some papers to see how to collapse them or pick the best one. And with regards to the script no one can comment unless you post it here and point out where you are stuck.

[qmarulfiz]

Thank you,

I've dabble with R and looks tutorial online. I think 2 weeks back I figure it out to convert the symbol in each array data through biomaRt producing appropriate gene symbol using probe gene.ID as filter.

Thanks again for the reply!

[badribio]

Happy to help