Error when calculating DE using the classical approach in edgeR
1
0
Entering edit mode
Rishav ▴ 20
@rishav-25031
Last seen 22 months ago
Patna

I am trying to use edgeR to analyze differential gene expression from my RNA-seq dataset and I get the following error, please help me out


# > y$samples
      group lib.size norm.factors
P105A     P 24065.56    1.0249858
P105D     P 21698.30    0.9844816
P106A     P 22661.48    1.0117203
P106D     P 20173.68    0.9969133
P112A     P 24056.76    1.0045940
P112D     P 22153.58    0.9952232
P131A     P 24592.05    0.9955994
P131D     P 21559.29    0.9901179
P138A     P 23581.63    1.0200888
P138D     P 21282.37    0.9919605
P140A     P 27497.28    1.0197013
P140D     P 21611.54    0.9944977
P152A     P 23479.47    1.0121774
P152D     P 22184.55    0.9937370
P157A     P 23430.98    1.0024456
P157D     P 21157.52    1.0011815
P158A     P 24895.99    1.0141776
P158D     P 21379.88    0.9920294
P161A     P 25416.33    0.9995592
P161D     P 20748.34    1.0132618
P16A      P 24177.85    1.0020082
P16D      P 21974.95    0.9942317
P170A     P 25725.95    1.0025857
P170D     P 20343.97    0.9936017
P171A     P 25292.65    0.9872262
P171D     P 20796.21    0.9984913
P176A     P 22787.21    0.9891168
P176D     P 19800.99    0.9945080
P179A     P 22356.75    1.0221736
P179D     P 20512.91    0.9917283
P49A      P 25526.92    1.0128244
P49D      P 21903.22    0.9856744
P62A      P 24692.72    1.0051444
P62D      P 22622.22    0.9918075
P6A       P 25424.87    1.0033799
P6D       P 24084.53    0.9857824
P75A      P 24040.41    0.9947503
P75D      P 20787.92    0.9998319
P94A      P 26799.46    0.9977988
P94D      P 21586.76    0.9915676
P99A      P 25772.66    1.0142671
P99D      P 21257.97    0.9854599
> y <- estimateDisp(y)
Using classic mode.
> sqrt(y$common.dispersion)
[1] 0.009882118
> et <- exactTest(y)

#  Error in exactTest(y) : 
  At least one element of given pair is not a group.
 Groups are: P
RNASeqR • 1.1k views
ADD COMMENT
0
Entering edit mode
ATpoint ★ 4.6k
@atpoint-13662
Last seen 9 hours ago
Germany

You only have one group. A pairwise comparison, as the name suggests, needs at least two.

ADD COMMENT
0
Entering edit mode

Please explain it further. I am unable to understand clearly

ADD REPLY
0
Entering edit mode

so, how can i create two groups

ADD REPLY
1
Entering edit mode

DEG analysis compares gene expression between two user-defined groups, e.g. two experimental conditions, are you aware of that? So, you as the analyst should know what the groups are. Are you familiar with the idea of DEG analysis, I am a bit confused about your question? What is your analysis goal, so the scientific question you want to answer.

ADD REPLY
0
Entering edit mode

Thank you so much for making me understand

ADD REPLY

Login before adding your answer.

Traffic: 633 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6