edgeR for with no Replicate
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@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 .

====================================

> 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

========================

edger without replicate • 3.0k views
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Yunshun Chen ▴ 900
@yunshun-chen-5451
Last seen 10 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.

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

 

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

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

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

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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 .

=============================

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'
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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.

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