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  • joxcargator73
    started a topic Comparing two RNAseq exepriments

    Comparing two RNAseq exepriments

    I am trying to compare significant expressed genes from two experiments.
    Basically I have this:
    Experiment 1: (Paired-end RNAseq)
    Control(bacteria in Minimal medium) (3 replicates)
    treatment1(bacteria with carbon source A) (3 replicates)
    treatment2 (bacteria with carbon source B) 3 replicates)

    Experiment 2: (Single-end RNASeq)
    Control(bacteria in Minimal medium) (3 replicates)
    treatment1(bacteria with carbon source C) (3 replicates)
    treatment2 (bacteria with carbon source D) 3 replicates)

    I conduct a first analysis of each experiment independently using DESeq and found the significant differential expressed genes.
    Now I wonder if there is a way to compare results from experiment 1 and 2 and avoid bias of batch effects.
    Can I analyzed exepriment1 and 2 together and correct for batch effect?
    or Can I just take experiment 1 and 2 separately as independent experiments and contrast the significant expressed genes in each case?.

    Thanks

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