Question: edgeR for with no Replicate
0
gravatar for Sushant Pawar
3.9 years ago by
Nashik
Sushant Pawar0 wrote:

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 • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Yunshun Chen510 • written 3.9 years ago by Sushant Pawar0
Answer: edgeR for with no Replicate
1
gravatar for Yunshun Chen
3.9 years ago by
Yunshun Chen510
Australia
Yunshun Chen510 wrote:

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 COMMENTlink modified 3.9 years ago • written 3.9 years ago by Yunshun Chen510

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

 

ADD REPLYlink written 3.9 years ago by Sushant Pawar0

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

ADD REPLYlink written 3.9 years ago by Sushant Pawar0

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

ADD REPLYlink written 3.9 years ago by Yunshun Chen510

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

ADD REPLYlink written 3.9 years ago by Sushant Pawar0

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'
ADD REPLYlink written 3.9 years ago by Sushant Pawar0
1

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 REPLYlink written 3.9 years ago by Aaron Lun25k
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