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Table 4 Expression data for low abundance genes

From: The bench scientist's guide to statistical analysis of RNA-Seq data

 

DESeq

edgeR

Raw Counts

RPKM

 

log2 FC

Padj

log2 FC

Padj

con1

con2

con3

trt1

trt2

trt3

Control

Treatment

Genes turned on

            

Glyma18g02680

Inf

0.0224

27.39

0.0187

0

0

0

5

1

4

0

0.08 ± 0.032

Glyma01g41980

Inf

0.0331

27.26

0.0187

0

0

0

3

4

2

0

0.30 ± 0.206

Glyma11g04880

Inf

0.0324

27.25

0.0187

0

0

0

5

2

2

0

0.17 ± 0.054

Glyma16g06500

Inf

0.0320

27.24

0.0326

0

0

0

5

1

3

0

0.14 ± 0.057

Glyma12g05780

Inf

0.0488

27.08

0.0326

0

0

0

3

1

4

0

0.06 ± 0.030

Genes turned off

            

Glyma07g02590

-Inf

0.0011

−28.11

0.0004

7

4

5

0

0

0

0.20 ± 0.050

0

Glyma17g17930

-Inf

0.0011

−28.12

0.0004

3

5

8

0

0

0

0.17 ± 0.084

0

Glyma17g34230

-Inf

0.0016

−28.02

0.0006

9

3

3

0

0

0

0.54 ± 0.292

0

Glyma12g14620

-Inf

0.0052

−27.71

0.0035

3

5

4

0

0

0

0.57 ± 0.372

0

Glyma03g37640

-Inf

0.0075

−27.56

0.0061

4

2

5

0

0

0

0.14 ± 0.013

0

  1. Log2 fold change, p-value, raw count data and RPKM vaules for representative samples from gene clusters turned on or off by elevated ozone. DESeq outputs an 'Inf' or '-Inf' log2 fold change value to excel when all control or treatment replicates map zero reads.