theory behind the differential expression

Question

[Mozart]

Hi guys, I'm getting into grip with R and the RNA seq analysis. In order to gauge my knowledge I had to deal with an "exercise" and compare my final results with a correct reference. Actually, I think I did a decent job as my final results seem to be confirmed but I need to double check few things with you guys..

So I had two different conditions (KO for a specific receptor and wild type). In the reference, as a final output, I have an excel file. I am actually not sure about what some these columns mean; so I wish this kind of jargon might be more familiar for you, guys:

Probe name|Symbol|Title|Chr| <- fine to me

Start|Stop|Strand|Type|Level|Other| <- not sure about those ones

example:

Start     |Stop     |Strand| Type           |Level |  Other|
873620     873640     +       protein coding   level=2   ---

Of course guys, I know the meaning of (some) of these columns but I would like to be more confident in the comparison with my results.

thanks in advance

[fr]

I'd say the documentation of the tool you are using should explain this in good detail for you to fully understand what is being reported, please indicate it in your post. My guess is, if you do not understand what is being reported in the log2FoldChange|pvalue_KO_vs_WT|padj_KO_vs_WT| lines, you should consider revising your statement on I think I did a decent job as my final results seem to be confirmed :)

Related: What is Differential Expression?

[Mozart]

thanks; sorry if this may sound annoying to you but these columns come from the (correct) reference/tutorial and my output columns are quite different as I carried out a different pipeline. so for example terms like level, strand, the adjusted pvalue between ko vs wt {so if for example could be linked to the Benjamini correction}. thanks anyway

[GenoMax]

Start|Stop|Strand|Type|Level|Other|

They are telling you start/stop/strand/type of the gene you are looking at. Level could mean something specific depending on program you are using/type of annotation.

If this is the result from DESeq2 then the result columns are described in vignette.