Hi everyone
So I had a question about the scde package in R which I am trying to use for single cell analysis. When I try to run it in R using the code below: source("https://bioconductor.org/biocLite.R") biocLite("scde")
I get warning message: package 'scde' is not available (for R version 3.2.3)
and I essentially need to use the scde.error.models function using: o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)
which as expected gives me the error that this function does not exist. My question is how can I get scde to work or if that is not possible, what should I be using instead?
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shg018 •
According to the warning you're getting
package 'scde' is not available (for R version 3.2.3)
looks like you'll want to upgrade your R version. Currently, R is at 3.4.1. I'd upgrade R and Bioconductor both to see if that fixes your problem. Good luck.
Thank you soo much!! That worked!
If you don't mind me asking, when I run:
o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1)
I am getting the error that arguments must have same length and error in tapply(...){. Which arguments does it refer to?
I haven't used scde.error.models() before, but I would guess it has to do with the counts or groups parameters. According to the documentation, counts should be
a read count matrix...the rows correspond to genes (should be named), columns correspond to individual cells.
So I would check if the columns of cd match what you've input as sg.
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