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Table 5 Number of transcripts declared differentially expressed (DE) using edgeR robust

From: Inferential considerations for low-count RNA-seq transcripts: a case study on the dominant prairie grass Andropogon gerardii

  All transcripts High-count transcripts Low-count transcripts
  Total SB-only BB-only Total Total SB-only BB-only
No filter 3173 248 126 40 2135 245 121
RP filtering 3177 248 126 40 2137 245 121
CPM filtering 1002 0 0 23 239 0 0
  1. The table contains the number of total transcripts, high-count transcripts and low-count transcripts declared DE using edgeR robust (with degrees of freedom specified based on the corresponding estimate obtained using classical edgeR software) analyses on the complete dataset (i.e. no data filtering applied) or following data filtering based on reads-present (RP) criterion or counts per million (CPM) criterion. Also listed are transcripts with expression levels present in sand bluestem and absent in big bluestem (SB-only transcripts) and transcripts with expression levels present in big bluestem and absent in sand bluestem (BB-only transcripts)