2
$\begingroup$

I'm following along with some pre written code to learn how to do differential expression. I am using the same data set and have gone back through the code and copy and pasted what they used and the follow along gets the two headings rather than the single one that I am getting, so I'm a bit confused how I'm getting different results.

I have some data which I have put through DESeq but the output for resultsNames isn't what I expect. The code is

dds <- DESeqDataSetFromMatrix(countData = exprs(bottomly.eset), colData = pData(bottomly.eset), design = ~ strain)
dds <- DESeq(dds)

but this code produces this output "Intercept" "strain_DBA.2J_vs_C57BL.6J" whereas the output that I intended was "Intercept" "strain_DBA.2J" "C57BL.6J"

Is there a simple way to change this within the code that I have or is this something related to the dataset I used?

Improve this question
$\endgroup$
2
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Jul 14, 2023 at 21:23
  • $\begingroup$ In your expectation, what is the DBA.2J strain tested against? $\endgroup$
    – Ram RS
    Commented Jul 14, 2023 at 22:04

2 Answers 2

Reset to default
2
$\begingroup$

DESeq2 is a package designed for calculating differential expression, in other words for comparing expression between two states. The primary results it produces are therefore comparative values (e.g. comparing DBA.2J and C57BL.6J in your case).

Given that this does not seem to be your intended calculation, it would be helpful if you could provide more context around what you want to use DESeq2 for. If it's not for differential expression, there's likely a better tool / approach for solving your problem.

Improve this answer
$\endgroup$
0
2
$\begingroup$

So I was following along with a coding lesson from Youtube learning how to do differential expression in R, if the data had been my own I probably would have been able to figure out what needed to be done. The code that worked for me was

dds <- DESeqDataSetFromMatrix(countData = exprs(bottomly.eset), colData = pData(bottomly.eset), design = ~ strain)

dds <- DESeq(dds, betaPrior = TRUE)

I was then able to use this code below which was resulting in the error previously contrast.deseq2 <- list(c("strainC57BL.6J", "strainDBA.2J"))

Thank you to everyone who commented on this question

Improve this answer
$\endgroup$
3
  • $\begingroup$ I don't understand the difference between this and the vs offered by DESeq2 previously in your question. Given that the default test is Wald and betaPrior is TRUE by default for Wald tests, how is this result any different? $\endgroup$
    – Ram RS
    Commented Jul 17, 2023 at 13:58
  • $\begingroup$ I'm not sure of the difference but this is the result I got when running the new code $\endgroup$
    – Sabrina
    Commented Jul 17, 2023 at 21:07
  • $\begingroup$ Run it both ways and see if the number of genes or fold change value differs by much. I honestly don't think there should be any significant difference. $\endgroup$
    – Ram RS
    Commented Jul 18, 2023 at 13:03

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.