Entering edit mode
3.6 years ago
3kixintehead
▴
10
I'm pretty new to R and rna-seq, so I'm not sure what the issue is here. I've mostly been following the RNA-seq workflow by Love et al. I'm really not sure what is causing this issue with my MA plot however. I started with imported counts from a csv instead of BAM or SAM files. I'm worried this decision messed me up from the start as I've run into problems at every point. My latest issue is that the MA plot I'm trying to perform has no x-axis. I have no idea why.
![No X - axis][1]: https://ibb.co/RpkJW9p
dds = DESeqDataSetFromMatrix(countData = cts,
colData = col_data,
design = ~ Condition)
ddsf <- dds[ rowSums(counts(dds)) > 1, ]
dds <- DESeq(ddsf)
res <- results( dds )
res <- lfcShrink(dds, coef="Condition_infected_vs_control", type="apeglm")
plotMA(res, ylim=c(-2,3))
I've tried several different approaches with the res dataset and I haven't been able to find this problem elsewhere. Does anyone have any tips? Thanks.
What package is that from,
DESeq2? Please add full code.Yes, it is DESeq2. What would be the most relevant parts? My code is kind of a mess as I've tried several approaches and I am just learning this technique.
Can you repeat the plot with
DESeq2::plotMA(res)? I think you are using code from a different package, this plot makes no sense.Interesting. That did give me X spread, and coloration. But the plot isn't symmetrical along the x-axis. I thought that was hallmark of MA plots?
I was just following the instructions written by Love et al and I saw the same code in a few other places too. I didn't know it was from another package!
Not necessarily, you can have more up- than downregulated genes or vice versa I would say. The important thing is that most genes are somewhat along y=0 which indicates proper normalization.
It is safer to use the package::function notation for functions that are used by multiple packages. plotMA is I think used by multiple other packages as well under the same name, but different code.
Thank you! Coming from Python (and being new to programming in general), R is a pretty difficult beast. None of the tutorials I was following mentioned that.