Question: edgeR negative bionomial error in without replicate data?
0
gravatar for 1234anjalianjali1234
12 months ago by
India
1234anjalianjali123430 wrote:

I am doing DEG analysis between two sample (Normal vs Treated) without replicates using edgeR:

library(edgeR)
data = read.table("MYFILE-counts.txt", header=T, row.names=1, com='')
bcv <- 0.2
counts <- matrix( rnbinom(40,size=1/bcv^2,mu=10), 20,2)

it is giving error:

## Warning messages:
1: In data(rnbinom(40, size = 1/bcv^2, mu = 10), 20, 2) :
 data set ‘rnbinom(40, size = 1/bcv^2, mu = 10)’ not found
2: In data(rnbinom(40, size = 1/bcv^2, mu = 10), 20, 2) :
 data set ‘20’ not found
3: In data(rnbinom(40, size = 1/bcv^2, mu = 10), 20, 2) :
 data set ‘2’ not found

I am not able to understand this error and need help to solve this. I know there is no significance of analysis without replicates, but i have no other choice.

Then i proceeded with:

counts <- data
y <- DGEList(counts=counts, group=1:2)
et <- exactTest(y, dispersion=bcv^2)

looking into the variable:

>y

An object of class "DGEList"
$counts
                     Normal.bam      Treated.bam
Cluster-0.0                  0      50
Cluster-1.0                  0      25
Cluster-2.0                  0      16
Cluster-2.1                  0       8
Cluster-3.0                  0      15


202654 more rows ...

$samples         group     lib.size      norm.factors
Normal.bam      1          3.22e+07              1
Treated.bam     2          1.05e+08              1

why there is norm.factor of 1 in both sample?

>et

    An object of class "DGEExact"
$table
            logFC logCPM   PValue
Cluster-0.0  8.03  -1.58 4.06e-05
Cluster-1.0  7.04  -2.39 2.13e-03
Cluster-2.0  6.40  -2.89 3.49e-02
Cluster-2.1  5.42  -3.58 7.51e-02
Cluster-3.0  6.31  -2.95 3.49e-02
202654 more rows ...

$comparison
[1] "1" "2"

$genes
NULL

Why there are NULL in $genes?

no-replicate edger rna-seq R • 414 views
ADD COMMENTlink modified 12 months ago by ATpoint39k • written 12 months ago by 1234anjalianjali123430
1

This works fine for me (no errors, no warnings):

bcv <- 0.2
counts <- matrix( rnbinom(40,size=1/bcv^2,mu=10), 20,2)

Check the size of matrix:

dim(counts)
# [1] 20  2

I am guessing you have some hidden characters in the code, try to retype the commands, instead of copy-pasting from some document/website?

ADD REPLYlink modified 12 months ago • written 12 months ago by zx87549.6k

I have tried typing it myself, but again giving same error. as suggested by you, i have checked my counts dimention:

> dim(counts)
    [1] 202659      2

i have tried this also but nothing worked:

counts <- data(rnbinom(40,size=1/bcv^2,mu=10), 202659,2)

i have modified my question.

ADD REPLYlink modified 12 months ago • written 12 months ago by 1234anjalianjali123430

Why are you using data instead of matrix?

ADD REPLYlink written 12 months ago by zx87549.6k

sorry it was by mistake. Even if i am using matrix instead of data, there is error:

counts <- matrix(rnbinom(40,size=1/bcv^2,mu=10), 202659,2)

Warning message:
    In matrix(rnbinom(40, size = 1/bcv^2, mu = 10), 202659, 2) :
    data length [40] is not a sub-multiple or multiple of the number of rows [202659]

Could you please explain the code, i think i am not able to set the parameters according to my dataset.

i tried:

 counts <- matrix(rnbinom(405318,size=1/bcv^2,mu=10), 202659,2)

this gives no error, but i need to understand, what this code is doing to my data and what parameter should be used like which value of mu should be taken.

Thankyou

ADD REPLYlink modified 12 months ago • written 12 months ago by 1234anjalianjali123430
1

To avoid first warning, we need to supply correct dimensions, try this code, and adapt numbers for nRows, nCols as needed:

nRows <- 4
nCols <- 2
counts <- matrix(rnbinom(nRows * nCols, size = 1/bcv^2, mu = 10), nrow = nRows, ncol = nCols)

Regarding mu, read the manuals, tutorials.

ADD REPLYlink modified 12 months ago • written 12 months ago by zx87549.6k

Hi 1234anjalianjali1234, I removed my comment, sorry I did not read your question properly, my bad.

ADD REPLYlink written 12 months ago by ATpoint39k

Actually i need some more answers related to this question. Should i post a new question or modify this one only?

ADD REPLYlink written 12 months ago by 1234anjalianjali123430
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