how to start DEG analysis after featurecounts

Question

[kayah]

[kayah]

i don't know how to start DEG analysis in R with this data. i usually analyze DEG by just raw data provided in Pubmed. but. this time i start to analyze data with RNA seq. so please help me

[ATpoint]

This is raw counts. Relevant parts is first columns with gene names and columns 7-end which is the counts per sample.

[kayah]

Thank u soooo much!! Then i need to extract first column and seventh column to analyze DEG???

[Gordon Smyth]

The DGEList() function in edgeR provides an easy way to distinguish annotation columns from counts. Just use the annotation.columns argument to specify the columns that are not counts.

Alternatively, the featureCounts2DGEList function converts Rsubread::featureCounts output directly to a form suitable for a DE analysis without writing any intermediate files to disk.

But in this case, I wonder why you are not using the genewise read counts for GSE210683 that are already provided on the GEO website. This is 3' QuantSeq data, so it is not standard RNA-seq.

[kayah]

I'm just practicing for learning RNA-seq flow! thank you for kind explanation!!