Error in vsd_adjusted_log2[rownames(subset(res, !is.na(padj) & padj < : subscript out of bounds

Question

[mrinsmrids]

Hi, I have been using DESeq2 , a BioConductor package to run a piece of code which runs the comparison between differentially expressed genes in D5 vs D7. But, unfortunately, I have been receiving an error that I have been trying to troubleshoot for a while right now.If anyone could help me figure this out, it would be great. I have attached the screenshot of the piece of code and the error in this post. I hope to hear from you as soon as possible.

The error:

Answer 1

[swbarnes2]

You can't just dump multiple blocks of code with no indication where the problem is. You have to spend more time than that when asking people for help. And why post a pic of your code instead of it being text?

As far as what you've shown, you just made up vsd_adjusted_log2 without actually having any data in it. Of course, no one can have any idea what's in it, because you chose not to put up any of its contents, while still expecting people to troubleshoot an object they can't see?

You need to remove this pic, and put up the smallest amount of code (use the code format button to make it more readable) which works until the problem.

[mrinsmrids]

Thankyou for getting back to me on this . So, I wanted to put the full piece of code there because there is a sense of continuity.If I were to show you what the vsd_adjusted_log2 graph is , then it goes way back and the code would be longer.But I will update with the smallest amount of code so that you get a better understanding.

But this is what the vsd_adjusted_log2 contains.

vsd_adjusted_log2 <- removeBatchEffect(assay(vsd), batch=vsd$Time_point, covariates = vsd$Age)