Error Estimating the NB Dispersion of a Dataset
2
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Entering edit mode
@humberto_munoz-10903
Last seen 7.8 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 • 2.1k views
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Entering edit mode
@ryan-c-thompson-5618
Last seen 8 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 7.8 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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