DESeq basics

[iketutgunarta]

Hi Mike, may God bless you for making this video (and other video). Your channel is give the best explanation I've seen so far.

[marcolicalzi]

Prolly the best RNA Seq analysis I've ever seen. Thank you!!!

[NazaninSekhavat]

very useful thank you. also could you please give us the link of the dataset so we could have a practice on it?

[milanbhattarai]

Wonderful Brother!! Simply Wonderful!! Love from Nepal

[lucast]

Our lab always had money to pay bioinformaticians to do all of our RNAseq analysis. Now we missed out on a grant and don’t have money to pay them, so I have to learn how to do it myself. Thanks a lot, this was very helpful.

[derekyuen]

Hi Mike ! This video helped me alot ! thank you !

[ghanbarmahmoodi]

HI Mike, Thank you so much for your great explanation. How I can download RNA seq from GEO to analysis based on the your method? thanks

[dr.suryanarayanrath]

hello, Mike excellent tutorial. Really, your video is a great contribution to students, faculties, and researchers who want to work in this field. Thanks as I have learned much from you. GOD bless you

[sebastianmihail]

I am doing a rna-seq analysis on sugarcane and Ive never touched R and today I made my first graph with Deseq2 thanks to you!!!!

[matthewseasock]

Amazing tutorial. I have been really trying to start learning R and this is the first tutorial I have found that starts with read counts and walks through DESeq2 in an accessible way. I really appreciate the education

[khanmohdsarim]

Hi Mike, Please suggest, As I have 4 sample (Control, Treatment 1, 2, and 3) with two condition of temperature and 3 replicate for each. How to put replicate 1, 2, 3 in columns? Should I use R1, R2, R3 of control of one condition and R1, R2, R3 of control of another condition.? Please suggest. Thanks

[amrsalaheldinabdallahhammo]

How DESeq2 calculates p-value, I know how the mean and LFC are calculated but how p-value is calculated? thanks

[Maryashahere]

Thankyou for your video Sir. Sir in your video the command write .csv; when it create, it just prints the number without "+enumber na", without this is it correct?

[jakebezzina]

Amazing tutorial!!!


For those who have a dataset with geneIDs such as entrez as the rownames and also want to annotate them before plotting, run this code after doing the resres[Order(res$padj), ] and write.csv function (using the same variables as in the tutorials, but pretending that the gene names aren't provided):

# Read the .csv function again so R Studio visualises it as a table (make sure to enable headers)
res.annotated <-

# Give annotated gene names to the corresponding entrez gene IDs in a row called "symbol"
res.annotated$symbol <- mapIds(org.Hs.eg.db, keys = rownames(res.annotated), keytype = "ENTREZID", column = "SYMBOL")

Edit: Make sure you have the annotation package ("org.Hs.eg.db" in this example) installed respective to your species and ID system: "Hs" for humans and "eg" for entrez genes.

DONE, you can now have annotated volcano plots!


This can be done for other IDs such as Ensembl For more info on annotations go to:

[mehdihjamadi]

please put the video for heatmap using complexheatmapk package for the differentially expressed genes. thanks

[Zineb]

Hi, thank you so much .
I have a question how did you make the first column as a row names? I get "duplicate 'row.names' are not allowed error' every time!!

[johirislam]

my data set is SARS-2 and control as like your water and 15psi.So in that case which one is equal to your condition??I am confused to interpret MA plot.Kindly help me in that case.

[GovardhanKShroff]

Thanks very much, really good explanation there Mike.

[souravchakraborty]

How are you setting up a notepad file to get two variables in the Coldata file? Please help me with this

[lucast]

Do you know of any good tutorials that show how to use Deseq for 4 groups at once instead of just 2? For instance, if I had A, B, C, D and I wanted to compare A vs B, A vs C, and A vs D. Is that pretty tricky?