Help! I have no replicate data. I spent a lot of time doing downregulated/upregulated and then do Pathway Analysis.
Method 1: Rsubread and the edgeR quasi-likelihood pipeline: it does not give me a Dispersion estimation. As a result, I can not continue to calculate res <- glmQLFTest(fit, contrast=B.LvsP) , neither pathway analysis
Method 2: DESEQ2 R does not calculate dds Link: https://bioconductor.org/packages/release/workflows/vignettes/RnaSeqGeneEdgeRQL/inst/doc/edgeRQL.html
Method 3:can not draw voom plot and gives error fit.cont <- eBayes(fit.cont). " no residual"
Method 4" Page 24 gives a solution for no replication data. I do not know what is housekeeping index is and what I should add to my R pipeline
y0 <- estimateDisp(y1[housekeeping,], trend="none", tagwise=FALSE) Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[': object 'housekeeping' not found
Method 5: it is not easy to follow hLink:https://www.rstudio.com/wp-content/uploads/2015/02/data-wrangling-cheatsheet.pdf
I appreciate it if you help me by example or by way to follow comments
Thanks in advance