Question: SCDE Package error
0
gravatar for shg018
4 months ago by
shg0180
shg0180 wrote:

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?

rna-seq R • 241 views
ADD COMMENTlink modified 4 months ago by erictleung90 • written 4 months ago by shg0180
2
gravatar for erictleung
4 months ago by
erictleung90
United States
erictleung90 wrote:

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.

ADD COMMENTlink written 4 months ago by erictleung90

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?

ADD REPLYlink written 4 months ago by shg0180
1

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.

ADD REPLYlink written 4 months ago by erictleung90
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