Question: R Script for selecting differentially expressed genes
1
gravatar for contato.carlosbau
4.2 years ago by
Brazil
contato.carlosbau10 wrote:

After trying some R scripts to generate DEG without success, I come here to make a simple question, where can I find an R script that calculates the differentiation expression of genes?

Recently I found a script in a book called Statistics and Data Analysis for Microarrays Using R and Bioconductor, and I tried the scripts found in that book, after some lines of code, the script stoped.

I tried also the generated script in GEO2R, I selected the serie and created 2 groups, normal and cancer, and started to make the comparison. I copied the code in the website and tried to reproduce in my pc, but without success, says an error about the object doesn´t have an numeric value. I emailed GEO2R about that, and I received a response saying that the developers were informed about it, hoping to hear from them soon. If the script of GEO2R works in local machines, I could use for all the series that I need, assuming that this script is reliable.

I´m trying to check DEG in normal an cancer cells, I appreciate the attention.

P.S - I modified all the R scripts that I came across to my needs, and made some modifications to see if I could solve it, but with no sucess until now.

microarray affy limma deg • 1.7k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by contato.carlosbau10
Answer: R Script for selecting differentially expressed genes
1
gravatar for Ryan C. Thompson
4.2 years ago by
Scripps Research, La Jolla, CA
Ryan C. Thompson7.4k wrote:

Every experimental design is slightly different, so it would be difficult to come up with a script that covers all possible cases while remaining simple and easy to use. Any script that covered all the necessary cases would end up being more complicated than simply writing the code yourself, so that's what I recommend you do instead: just write your own script. Start with a similar-looking example from the user's guide of whichever package you want to use (edgeR, DESeq2, limma) and adapt it to your experiment.

ADD COMMENTlink written 4.2 years ago by Ryan C. Thompson7.4k
Answer: R Script for selecting differentially expressed genes
0
gravatar for contato.carlosbau
4.2 years ago by
Brazil
contato.carlosbau10 wrote:

Thank you for your response! I will do that, I will use limma, since is with this package that I was trying since the beginning of my studies, and was the package that people told me to use it in the first place!! My concern was about the reliability of the script to for deg in normal vs cancer cells, since I came across a few diferente ones. So, to check for DEG comparing normal vs cancer cells I can choose a script for it? I thought to do that I have to do it in only one way. You see, GEO2R has the same script for any serie you might choose in GEO, of course that the only changes are the series and the number of groups that people may create it. And I came across with different ones , and some of them with different results, which now I assume that was for other purposes. Can I say that the GEO2R script is the best to check for DEG? Or more reliable ? Since you said that I can create my own, the reaults must be equal if other create or use different code but with the same goal right? Of course, using the same nornalization . Thank you again for your attention. P.S - I am working with the GEO samples and of course using the cells files that are in the database.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by contato.carlosbau10
1

If you don't give specifics, then I can only give general advice. The GEO2R script that uses limma for differential expression is a reasonable way to go about testing for differential expression in simple experimental designs, and you appear to have such a design. If you edit your question to show the exact code you are using and the exact error you are getting, we might be able to offer specific advice: http://bioconductor.org/help/support/posting-guide/

ADD REPLYlink written 4.2 years ago by Ryan C. Thompson7.4k
Answer: R Script for selecting differentially expressed genes
0
gravatar for contato.carlosbau
4.2 years ago by
Brazil
contato.carlosbau10 wrote:

Thank´s everyone for the answers, it was really helpfull. I tried for a few days some scripts and some tests, but no success yet.

My problem is the following: I am using the genereted GEO2R script for finding differentially expressed genes between cancer and treatment.

The script is working fine, because it downloads the samples from GEO (which is normalized with GCRMA), BUT what I am trying to do is run the script with my samples normalized with RMA.

So I thought just to change some things in the script to use my files instead of GEO. It didn´t work, because the function getGEO downloads a different file than CEL files, so I though just to change the values inside the downloaded file and run the script again, which didn´t work.

gset <- getGEO("GSE7696", GSEMatrix =TRUE)

It downloads a txt file with some information about the samples and all the values from all the cel files in the serie. And with some settings he determines which samples to contrast.

sml <- c("X","X","X","G1","X","X","X","X","X","X","X","X","X","X","X","X","G0","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X","X");

..
..
..
cont.matrix <- makeContrasts(G1-G0, levels=design)

As I said before, it works with the files downloaded from geo through getGEO function.

My question is how to use my cel files in the gset object?

I am using GEO2R script because I think is a good script to check for DEG, since I need the GCRMA and RMA to verify some differences, I guess what I am trying to find is how can I insert my cel files into the gset object, or turn into a GSEmatrix.

Thank you all again and sorry if I didn´t make myself clear

ADD COMMENTlink written 4.2 years ago by contato.carlosbau10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 416 users visited in the last hour