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I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company

This is how my meta data look

> head(meta)
           batch group    sex
30678.009 batch2     C   Male
30678.010 batch2     C Female
30941.001 batch1     C Female
30941.002 batch1     C   Male
30941.003 batch1     C   Male
30941.004 batch1     C   Male
> tail(meta)
           batch group    sex
30941.016 batch1    LT Female
30941.017 batch1    LT   Male
30941.019 batch1    LT   Male
30941.022 batch1    LT Female
30941.023 batch1    LT   Male
30941.024 batch1    LT Female
>   

I want to extract differentially expressed RNAs between my two groups without batch effect

I am doing this

Is this correct please?

dds <- DESeqDataSetFromMatrix(countData = count,
                              colData = meta,
                              design= ~ batch + group)

dds <- DESeq(dds, test="LRT", reduced=~batch)

res <- results(dds)
resultsNames(dds) 

[1] "Intercept"              "batch_batch2_vs_batch1" "group_LT_vs_C"         
> 
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1 Answer 1

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If both batches contain replicates of both groups (LT and C) then the presented code is what you should do, exactly pointed out in the vignette for the LRT: http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#likelihood-ratio-test

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    $\begingroup$ Thank you. Please, what do you mean by "If both batches contain replicates of both groups (LT and C)" ? I know each sample is one independent person and we have sent samples to Qiagen in two times $\endgroup$
    – Zizogolu
    Commented Jan 24, 2023 at 10:14
  • 1
    $\begingroup$ It means exactly like it reads. Both batches need to contain replicates (preferably in comparable numbers) of both groups. Use table(meta$batch, meta$group) to see the distribution contingency table. $\endgroup$
    – Ram RS
    Commented Jan 24, 2023 at 21:24

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