Gene expression of a particular gene

Question

[rajdeepboral00]

I have got the counts matrix fof my RNASeq data, and i have used DESeq2 for comparison and extracted the normalised counts of each of the samples. I want to see the expression of a particular gene for say x, I had subset the normalised counts for my gene x and drew a box plot, what kind of statistical test should i perform to check for its significance between groups?

Answer 1

[ATpoint]

Use DESeq2 and take this stat. I see no point in doing individual per-gene tests, it is known that these are underpowered in many cases. Just plot the gene and put the DESeq2 stats on top.

[rajdeepboral00]

I have in total 6 groups...and how can I compare between them

[ATpoint]

Please read the DESeq2 manual, I see do point repeating here what is already in there. Feel free with specific questions once you went through it in detail.

[Qroid]

This is a common step to be at. I'd recommending stepping back from the data and defining what you want answered. eg. Do you want to compare pairs of groups, maybe each group versus a control group? Do you want to answer whether the gene varies at all across all 6 groups? Do you want to compare groups AB vs CD and EF, etc.

Usually the biology/experimental design will dictate some obvious, meaningful group comparisons.

Settling on a question(s) will let you define the comparisons which will determine what you need to do in DESeq2. https://rdrr.io/bioc/DESeq2/f/vignettes/DESeq2.Rmd section "Differential expression analysis" has some basics on this, and looking up other DESeq2 vignettes with "comparison" and "contrast" examples will help. If it's still unclear you could try asking a more focused question. Good luck!

[Santosh Anand]

You should run DESeq and determine the appropriate contrast for the groups you are comparing. Refer to my response to your other question for details on how to identify the correct contrast: DESeq2 analysis