I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients[, coef] : subscript out of bounds from topTable as if it is not recognizing the condition I am asking it to return the top ten DEGs of. I have provided a bit more context and some descriptions of my variables below. Let me know if you need any more information or if anything is unclear.
Variables:
dge is a DGEList object of RNA seq data.
dge$counts is the raw counts.
dge$samples$dge_meta is the metadata and log2 transformed counts.
> colnames(dge$samples$dge_meta)
[1] "Lab.sample.ID"
[2] "Accession.Number"
[3] "Alias.used.in.some.figures"
[4] "Developmental.stage"
[5] "Infected"
[6] "Batch"
[7] "Trimmed"
[8] "Number.of.reads.that.pass.Illumina.filter"
[9] "Total.number.of.reads.mapped"
[10] "%.of.total.reads.mapped"
[11] "Reads.mapped.to.T..cruzi.Esmeraldo.haplotype"
[12] "Reads.mapped.to.hg19"
[13] "%.of.mapped.reads.belonging.to.T..cruzi.Esmeraldo.haplotype"
[14] "%.of.mapped.reads.belonging.to.hg19"
[15] "sample"
[16] "hpi"
Lastly keep_it is a binary vector used to filter our zero count genes.
Code:
mm <- model.matrix(~~hpi*Infected, data = dge$samples$dge_meta) #making our design matrix
more_than_1cpm_model <- voom(dge$counts[keep_it,], mm, plot = TRUE) #this one is filtered by the 25% greater than 1 cpm
cutoff <- 1e-05
empBayesfit <- eBayes(fit_gt1cpm)
topTable(empBayesfit,
coef = c("Infected"),
p.value = cutoff, number = 10)
Error message:
Error in fit$coefficients[, coef] : subscript out of bounds
To understand the context better I ran rlang::last_error and rlang::last_trace as well.
> rlang::last_error()
<error/dplyr_error>
arrange() failed at implicit mutate() step.
* Problem with `mutate()` input `..1`.
x Input `..1` must be a vector, not a `standardGeneric` object.
i Input `..1` is `samples`.
Backtrace:
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/dplyr_error>
arrange() failed at implicit mutate() step.
* Problem with `mutate()` input `..1`.
x Input `..1` must be a vector, not a `standardGeneric` object.
i Input `..1` is `samples`.
Backtrace:
x
1. +-dplyr::arrange(x, samples)
2. +-dplyr:::arrange.data.frame(x, samples)
3. | \-dplyr:::arrange_rows(.data, dots)
4. | +-base::withCallingHandlers(...)
5. | +-dplyr::transmute(new_data_frame(.data), !!!quosures)
6. | \-dplyr:::transmute.data.frame(new_data_frame(.data), !!!quosures)
7. | +-dplyr::mutate(.data, ..., .keep = "none")
8. | \-dplyr:::mutate.data.frame(.data, ..., .keep = "none")
9. | \-dplyr:::mutate_cols(.data, ...)
10. | +-base::withCallingHandlers(...)
11. | \-mask$eval_all_mutate(quo)
12. +-dplyr:::abort_glue(...)
13. | +-rlang::exec(abort, class = class, !!!data)
14. | \-(function (message = NULL, class = NULL, ..., trace = NULL, parent = NULL, ...
15. | \-rlang:::signal_abort(cnd)
16. | \-base::signalCondition(cnd)
17. +-(function (e) ...
18. | \-rlang::abort(...)
19. | \-rlang:::signal_abort(cnd)
20. | \-base::signalCondition(cnd)
21. \-(function (cnd) ...
