Thanks for your comment. Actually, I am looking for answers to the point. There are many posts showing what is up or down regulated etc (for example Understanding up and down regulated genes from LOG2 foldchange or foldchange) I did not find any example to show how to perform DE on a microarray data.
To be honest, firstly I was trying to do GSEA but in my previous post, they said GSEA is not the right technique since I did not have a good phynotype question or something like this. I believe all those functions you mentioned are for GSEA which I am not looking for. I simply look to find an example of how to find up/down regulated of a given microarray data.
You maybe want to try DESeq to find differential expressed genes across your samples. I recommend you to follow this manual. It is quite clear, and you can find all the steps explained and also the commands that you need to use in R. Here also there is a nice blog which explains how to use DESeq and take nice plots of expression data.
No, op is working with microarrays!
Oh! Sorry, I did not read that. Therefore ignore my comment! :)
OP should be adding more relevant tags. I say we abolish the "gene" tag. Most of the stuff in here is obviously related to genes!
I could not get the point across, Michael! Can you please explain what is op? Where to find it? Is there any example?
OP = Original Poster = you, Mohammad. You should be adding a lot of relevant details and disambiguation statements in your question. Mentioning that the post is important to you alone will not suffice if the question does not give folks a clear context of your problem setting.
Thanks. For sure, I'll try to be more specific in my other questions. Please let me know if anything is unclear here. I found the admin has changed the tags and added more into it. I did not mean the question is very important only for me, I know many people will face the same problem as I did (this is a very first step in gene analysis to find out which genes are up or which are down regulated) so I think this is an important question. I wrote that I could not perform DE and therefore, I share my problem here to see whether somebody has a solution or has an experience with this type of analysis. I also posted an example data set. I don't know how I can be more specific in this question. Please let me know, I try to explain more.
Thank you.
Being specific helps because you're starting out with data that a lot of people use, methods that a lot of people use, and are looking to get to a result that lot of people also have as their destination.
However you're looking for someone that belongs to all three groups, so if you mention a) microarray, b) Diff Expression analysis and c) list of up-regulated and down-regulated genes, and then explain the problem you're facing, people can tell you how to solve it, and even if you approach is appropriate or needs change.
This has been my experience asking questions on forums.