Error Estimating the NB Dispersion of a Dataset
2
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Entering edit mode
@humberto_munoz-10903
Last seen 6.1 years ago

I am following the user guide to estimate the dispersion of a dataset and got the following error messages:

> Patient <- factor(c(8,8,33,33,51,51))
> Tissue <- factor(c("N","T","N","T","N","T"))
> data.frame(Sample=colnames(y),Patient,Tissue)
  Sample Patient Tissue
1     8N       8      N
2     8T       8      T
3    33N      33      N
4    33T      33      T
5    51N      51      N
6    51T      51      T
> design <- model.matrix(~Patient+Tissue)
> rownames(design) <- colnames(y)
> design
    (Intercept) Patient33 Patient51 TissueT
8N            1         0         0       0
8T            1         0         0       1
33N           1         1         0       0
33T           1         1         0       1
51N           1         0         1       0
51T           1         0         1       1
attr(,"assign")
[1] 0 1 1 2
attr(,"contrasts")
attr(,"contrasts")$Patient
[1] "contr.treatment"

attr(,"contrasts")$Tissue
[1] "contr.treatment"

> y <- estimateDisp(y, design, robust=TRUE)
Error in locfitByCol(loglik, covariate, span = span, degree = 0) : 
  locfit required but is not available
> y$common.dispersion
NULL
> y <- estimateDisp(y, design, robust=FALSE)
Error in locfitByCol(loglik, covariate, span = span, degree = 0) : 
  locfit required but is not available
> plotBCV(y)
Error in plotBCV(y) : No dispersions to plot
>

Any suggestion to fix the error will be appreciated. 

dispersion edgeR • 1.6k views
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Entering edit mode
@ryan-c-thompson-5618
Last seen 23 months ago
Scripps Research, La Jolla, CA

The error message is telling you that you need to Install the locfit package. So do that and try your code again.

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Entering edit mode
@humberto_munoz-10903
Last seen 6.1 years ago

Thanks so much

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Entering edit mode

You might like to look at this post about suggested packages: should statmod be a dependency of limma and not a suggests?

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