Question: When should you use SVA vs. ComBat?
1
gravatar for chengzhao41
4.0 years ago by
chengzhao4180
Canada
chengzhao4180 wrote:

Hi, 

I'm looking for some advice and tips on when to use SVA vs. ComBat for homogenizing microarray gene expression data. 

Thanks,

Cheng

batch effect combat sva • 3.1k views
ADD COMMENTlink modified 4.0 years ago by Devon Ryan88k • written 4.0 years ago by chengzhao4180
6
gravatar for Devon Ryan
4.0 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

N.B., I'm being a bit loose with terminology below, but that should still suffice.

Combat is used when you know how the batch effect is structured. For example, you have microarrays prepared and run at different dates, where you expect "date" to cause a change in and of itself. SVA is used when you suspect that your data has underlying variation that's not being caused by the biology you're interested in or factors that you can easily identify. This often happens when there are a combination of background effects affecting your data, but you don't know about them and aren't remotely interested in studying them.

ADD COMMENTlink modified 12 weeks ago by RamRS20k • written 4.0 years ago by Devon Ryan88k
3

In short: If you know a covariate that drives the batch effect, use ComBat. If you don't, use SVA.

ADD REPLYlink modified 12 weeks ago by RamRS20k • written 4.0 years ago by brentp22k

Are there better methods for removing batch effect in R than ComBat, or is that still a preferred method?
I seem to be having some "batch effect" but it relates more to sample prep as all were run on the same chip, but I want to be sure I'm analyzing correctly.

ADD REPLYlink modified 12 weeks ago by RamRS20k • written 23 months ago by susanna.downing0
0
gravatar for kangyueapril
4.0 years ago by
kangyueapril80
United States
kangyueapril80 wrote:

They are same thing. In sva package, the combat method is contained. You can use combat in sva package. Beside, there are some other useful function in sva about adjust batch bias.   

ADD COMMENTlink written 4.0 years ago by kangyueapril80
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2060 users visited in the last hour