Question

edgeR for with no Replicate

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Sushant Pawar • 0

@sushant-pawar-9287

Last seen 7.9 years ago

Nashik

Hi all,

(edgeR Page no. 21,22 User Guide)

I am running program of edgeR for without replicate . I am getting one one error so please help me in that .

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> bcv=0.2
> library(edgeR)
> counts=matrix(rnbinom(40,size=1/bcv^2,mu=10),20,2)
> y=DGEList(counts=counts,group=1:2)
> et=exactTest(y,dispersion = bcv^2)
> et
An object of class "DGEExact"
$table
       logFC   logCPM    PValue
1 -0.4284000 15.82489 0.6982242
2 -0.2791370 16.10715 0.8677253
3  0.2291273 15.68416 1.0000000
4  0.8075674 15.98288 0.3752598
5 -0.2777101 15.62054 0.8292796
15 more rows ...

$comparison
[1] "1" "2"

$genes
NULL

> y1=y
> y1$samples$group=1
> y0=estimateCommonDisp(y1[housekeeping,])
Error in y1[housekeeping, ] : 
  error in evaluating the argument 'i' in selecting a method for function '[': Error: object 'housekeeping' not found

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edger without replicate • 3.0k views

ADD COMMENT • link updated 8.9 years ago by Yunshun Chen ▴ 890 • written 8.9 years ago by Sushant Pawar • 0

score 1 · Answer 1 · 2015-12-22

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Yunshun Chen ▴ 890

@yunshun-chen-5451

Last seen 2 days ago

Australia

The error message reads: object 'housekeeping' not found. Clearly you haven't defined housekeeping.

In the edgeR user's guide, it reads "For example, suppose that housekeeping is an index variable..." You can not simply copying the code from the user's guide and expect it to run without defining the object.

ADD COMMENT • link 8.9 years ago Yunshun Chen ▴ 890

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is it should be the vector or single gene name . give some example

ADD REPLY • link 8.9 years ago Sushant Pawar • 0

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is it should be the vector or single gene name ? . give some example

ADD REPLY • link 8.9 years ago Sushant Pawar • 0

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It should be an index variable (a vector of row indices).

ADD REPLY • link 8.9 years ago Yunshun Chen ▴ 890

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but what type of Genes we should store in that variable ?

ADD REPLY • link 8.9 years ago Sushant Pawar • 0

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Actually i am new to this field ,

I have add this to gene. again i am getting some warning . so please help me .

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housekeeping=c("REG3A","GP2")

> housekeeping=c("REG3A","GP2")
> y0=estimateCommonDisp(y1[housekeeping,])
> y$common.dispersion=y0$common.dispersion
> et=exactTest(y)
There were 50 or more warnings (use warnings() to see the first 50)

  full precision may not have been achieved in 'qbeta'
44: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
45: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
46: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
47: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
48: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
49: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'
50: In qbeta(0.5, alpha1[!all.zero], alpha2[!all.zero]) :
  full precision may not have been achieved in 'qbeta'

ADD REPLY • link 8.9 years ago Sushant Pawar • 0

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Estimating the dispersion from two housekeeping genes is not reliable. You need a decently sized set of about 50 - 100 genes that are expected to be constant across most biological conditions. Things that come to mind are actin, core metabolic proteins, etc. REG3A and GP2 would not be obvious choices.

ADD REPLY • link 8.9 years ago Aaron Lun ★ 28k