Question: RNA sequencing data batch effect removal
0
gravatar for Tenghui Chen
2.9 years ago by
Tenghui Chen0 wrote:

Hi All,

Recently I am trying to analyze some RNA sequencing data and perform the differential expression analysis. Since the sequencing data were generated in different times (experiments), I am worrying about the potential batch effects and would like to find a way to figure out and remove it (remove is more important!)

I tried to process the data in two different ways: 1) Obtain the RSEM values and perform the differential expression analysis, in this way, can anyone kindly provide a good tool to apply on RSEM values to remove the batch effect? 2) Obtain the htseq raw counts and use Deseq2 to perform the differential expression analysis. I saw previously another discussion about about justifying the batch effect by adding the 'batch' in the 'design' [design ~ batch+treatment] parameter in Deseq2. Besides this, can anyone kindly provide another good way to remove the batch effect?

Thanks for the help in advance.

batch effect rna-seq • 6.4k views
ADD COMMENTlink modified 2.9 years ago by Ron970 • written 2.9 years ago by Tenghui Chen0

When you cluster the samples, or do PCA analysis, do you see batch effects as confounding ? I am just curious.

ADD REPLYlink written 2.9 years ago by geek_y9.9k

Yes, I did PCA, but it did not really show very obvious batch effect, may because I just have very few sample size in each batch (from 2 to 5).

ADD REPLYlink written 2.9 years ago by Tenghui Chen0
1
gravatar for Ron
2.9 years ago by
Ron970
United States
Ron970 wrote:

Here is an example using "sva" package:

http://www.bioconductor.org/help/workflows/rnaseqGene/#batch

Remove Batch Effect From RNAseq with SVAseq and Combat

Also,you can use EdgeR.(Example by Devon).Its actually similar to using DESeq.

edgeR: Correct pipeline for DE analysis with multiple conditions and batches

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ron970

Thank you. I do not actually quite understand how to achieve a best practice with SVAseq. Do you know how to decide the n.sv value in the function?

ADD REPLYlink written 2.9 years ago by Tenghui Chen0
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