Search
Question: Single cells batch effects
1
gravatar for riccardo
7 months ago by
riccardo40
riccardo40 wrote:

Hi, I have single cells data from  two different experiments and I would like to remove the batch effects from the data in order to cluster correctly the cells. I would like to try to see what are the differences removing the batch effects due to housekeeping genes and also to try to remove the batch effects that are not specifically due to the housekeeping genes.

I think that you can do it for the bulk RNA seq using RUV but I would like to know if I can apply RUV using single cell data or if I have to use another method.

Thanks.

Best.

Riccardo

ADD COMMENTlink modified 7 months ago • written 7 months ago by riccardo40
2
gravatar for Aaron Lun
7 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

I would say that RUV is not the appropriate tool here. RUV(seq) is designed for detecting unwanted factors of variation. But in this case, you know the factor of variation - the batch/experiment in which each cell was processed. There's not much point running RUVseq to recover something that you already know.

Moreover, if you treat cells from the same batch as "replicates" and run RUV on the expression data within each batch, it will identify the population structure as unwanted factors and remove it. This will remove differences associated with cell types and states, which are presumably what you're actually interested in.

If your two experiments are replicates of each other (i.e., generated from the same tissue/cell line/condition), you can just run removeBatchEffect (from limma) to eliminate the batch effect prior to clustering. If your experiments are from entirely different conditions, the technical and biological effects are confounded with each other, and there isn't much you can do to remove the former without also discarding the latter.

I didn't understand your point about house-keeping genes, but it doesn't seem particularly relevant.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Aaron Lun17k
0
gravatar for riccardo
7 months ago by
riccardo40
riccardo40 wrote:

Hi thanks for the advices!

About house-keeping genes I did not explained myself very well. I wanted to put the house-keeping genes as negative control in RUV.

Thanks.

ADD COMMENTlink written 7 months ago by riccardo40
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 2.2.0
Traffic: 272 users visited in the last hour