Question: rlog transformation for Time-course data
0
gravatar for veigh09
3.1 years ago by
veigh090
Beijing
veigh090 wrote:

Hi !

I foundĀ rlog transformation method in DESeq2 package was very useful for clustering RNA-seq data.

Recently, I was dealing with some time-course data, and ready to run a co-expression network analysis via a R package, which recommends a variance-stabilizing transformation. I'm wondering how to do rlog (vst) for time-course data.

For example, if I have three time-points, Day0, Day1, and Day2, shall I just take the Day0 sample as untreated sample (Day1 and Day2 sample as treated samples), then simply call the rlogTransformation function ?

Thanks so much.

ADD COMMENTlink modified 3.1 years ago by Michael Love26k • written 3.1 years ago by veigh090
Answer: rlog transformation for Time-course data
2
gravatar for Michael Love
3.1 years ago by
Michael Love26k
United States
Michael Love26k wrote:

hi,

Yes you can just use vst() or rlog() functions in order to produce variance stabilized data. You don't need to provide sample information or define which one is the treated or untreated.

You can take a look at the plots we have in the DESeq2 vignette and see which transformation you prefer. If you need, the matrix of values from a DESeqTransform object can be extracted with assay() function.

ADD COMMENTlink written 3.1 years ago by Michael Love26k

Thanks for your help, Michael.

ADD REPLYlink written 3.1 years ago by veigh090
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