Dear everyone,

currently I am writing my master thesis which deals with the expression of genes during microsclerotial germination of the phytopathogenic fungus Verticillium longisporum. My next task is to conduct a bioinformatical analysis, the first step of which consists of creation of an OrgDB database. When I try to implement my supervisor's guidelines, I am constantly facing error messages which I do not understand and when I search the Internet, I do not understand the advice either (possibly due to a lack of basic knowledge). Therefore, I would be very pleased to find someone to explain precisely how to create an OrgDB database and how to conduct a basic bioinformatical analysis of gene expression. I would strongly appreciate your support because I absolutely do not know how to solve this problem. Thank you very much!

The instructions for creating the OrgDb already exist. You can load the AnnotationForge package and then look at ?makeOrgPackageFromNCBI which explains all the arguments for the function and has an example as well. There is also a vignette. As for the analysis of gene expression, it's dependent on what sort of data you have (and which you neglect to mention). If you have RNA-Seq data, you can read either the edgeR user's guide, or the DESeq2 vignette. If you have microarray data, then the limma user's guide is what you should read. There are also various educational resources you can look through.

Having once been new to this field, I understand your frustration. It is annoying to try to do something and get error messages in return. That said, you are asking for something that is not available, either here or on any other possible support site. This site is meant to help people who have specific questions about Bioconductor software, not as a training site intended to walk people through a particular analysis. Learning how to do something, particularly using Open Source software, is mostly something you have to learn for yourself. There are many sources of information out there, but in the end you have to read all that stuff, comprehend what you are reading, and then apply what you have learned.

Dear Mr MacDonald,

thank you very much for your answer! I have already tried to load the AnnotationForge package, but that did not work. Therefore I would appreciate your help. Further, I am using delta Ct values for examining gene expression as well as mRNA transcript sequences. By the way, I have been trying to learn that stuff for myself for three years now and have given up several times, but it seems inevitable as a part of my study program. Unfortunately, when I read the stuff, I do not comprehend anything that I am reading. Therefore, I would be very pleased to find someone here who gives me some training.

Kind regards