Hello all, I am new here and have a potentially unusual question: In an internship I am working on Bulk RNA Seq data from Drosophila where I have a KO and WT variant sequenced at 10d or 30d of age. In this time the flies go from pre-symptomatic to symptomatic and I want to extract clusters of genes that behave differently over time (e.g. "these 30 genes go down over time in KO, but stay high in WT").
A company has done the analysis before I was here and I only have the results_apeglm.xlsx output for each timepoint (KOvWT 10d and KOvWT 30d), which gives me TPMs, P-values and LFCs but not much more to work with. In the link I put a snippet from the Excel sheet, so you can get an idea: Snippet RNASeq KOvsWT 10d 30d
I wanted to use degPatterns() from the DEGreport package, but cannot get it to work so far. I just can´t figure out how to transform my data into a format that is accepted by the package, as the example in the vignette uses a totally different object class. I already converted everything into a log2 transformed expression matrix, but I can´t figure out how to provide degPatterns with the descriptors it wants to have.
It is highly appreciated if someone could help me out with the use of this package or suggest a different one to use.
Thanks a lot for your time! All the best, Paul
Do you have access to the raw count matrix? It will be more accurate (and easier) to just run DESeq2 on the raw counts and explore the interaction KO:Day which you are interested in.
Sadly I have just the pre-digested format of the DEGs in the Excel sheet. But if nothing can be done, I will ask my supervisor do contact the company so I get the raw matrix.
In any case, when you'll want to publish it you'll have to deposit the raw sequencing data. It's frustrating that the company didn't deliver the desired answer though.
Yes...I just tried to mail them and hope they will respond quickly. Last time it was rather slow. I will just reply to the thread whenever I have any news (their lists of degPattern genes, raw counts...) Thank you for replying so fast!