Skip to main content

Table 1 Number of DEGs selected by FC, SAM and t-test and different cutoff

From: Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis

 

AFX_1

AFX_2

AFX_3

AG1_1

AG1_2

AG1_3

ILM_1

ILM_2

ILM_3

|log2FC| > 1 (p < 0.01)

4442

4236

4546

5405

5601

5460

3677

3355

3281

|log2FC| > 1 (p < 0.05)

4444

4237

4548

5539

5736

5554

3677

3361

3281

SAM (P < 0.01)

4665

4269

3726

2623

2658

2840

5192

3059

6996

SAM (P < 0.05)

6682

6485

6287

5495

5553

5692

6634

5657

8071

t-test (p < 0.01)

9246

9322

9528

7447

8209

8180

7757

6497

7036

t-test (p < 0.05)

9920

9982

10187

8302

8925

9018

8649

7642

8021

  1. There are three microarray platforms, and three test sites for each platform. For the convenient of intra- and inter-platform comparison, we directly focused on the expression of 12,091 common probes based on matching of One Probe-to-One Gene List summarized by MAQC project (http://www.nature.com/nbt/journal/v24/n9/extref/nbt1239-S5.txt). DEGs were selected by three different statistical methods for enrichment analysis, namely fold change ranking with a non-stringent p-value cut-off, SAM and t-test. Different cutoffs were applied in this research.