Hello everyone. As i am interested in doing differential gene analysis of microarray dataset from GEO, i started to reproduce some articles following their methods. I tried different bioconductor packages like limma, affy for deg analysis but writing code seems very difficult to me. Most of the articles used limma package for deg. 1. Could you suggest me any tools that perform preprocessing, qc, normalization and deg at the same platform? 2. I tried different online pages and videos for practising limma in R studio. But i didn't get any link that perform detailed microarray analysis. Could you provide me all the codes (limma) for complete microarray analysis (preprocessing, qc, normalization and deg)? 3. After performing GEO2R analysis, i opened the file in excel, filter them using p value/adjusted p value, delete rows with empty gene name and remove duplicate genes for identifying deg. Is it ok?
The answer to all questions is: Please read the limma manual.