Total count filter cutoff-edgeR
Hello,
I'm using edgeR for analysis of may data and I'm not sure what total count filter value cutoff value I should use, My reads are paired 50bP reads and total reads per sample is about 80,000,000. I tried cutoff values of 5,10,15,30,50 and 100 and I only saw differences between 50 and 100 but still looking for logical reason to choose the cutoff value.
Appreciate your help,
Mahnaz
• 2,286 views
•
link
updated
by
Devon Ryan
•
written
by
mahnazkiani
•
written
by
mahnazkiani
1 answer
Just us the genefilter package and it'll allow you to determine the optimal threshold. I recommend reading the paper describing it as well as it gives the underlying justification.
• 0 views
•
link
written
by
Devon Ryan
Log in to answer this question.
More posts like this
-
Stacks error:failed to gz-open
written by mahnazkiani
-
Strange mapping on miRNAs from RNA-seq library
written by manekineko
-
Concerning FDR calculation using Limma
written by sebastien200109 •
-
Piping samtools commands
written by jyu429
-
Trimming fastq with quality
written by RafaelMP
-
Depth of RNAseq with sensitive detection
written by sckinta
-
Genomic Coverage - Samtool's undocumented "depth" verses the poorly documented pileup.
written by John
-
QC based on Samtools Flagstat
written by indranipoddar •
-
theta value and R value in SNP data
written by ftp
-
Quality Contol For Illumina Transcriptome Reads
written by Plantae
