Hi everybody,
I want to analysis gene expression in GEO2R from NCBI, but GEO2R just analyze dataset that have biological replicates (pair data). of course, I have experience in R for affymatrix data using bioconductor from this case study (http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/) that is CEL format but I need other scripts in R to do other format (txt data) for other kind of platforms of microarray like 3D oligo chip thus I try this ([https://www.biostars.org/p/148471/) but it is not worked. So, main question is, can someone guide me how I can proceed with limma or other packages in R, if I have data that is txt format and do not affymatrix with no biological replicates (for example GSE56875) in such format? I think if we can do some alteration in GEO2R script to do single datasets, it would be success
Many Thanks in advance
