Hi Everyone,
I am working on a set of bacterial RNAseq data (generated using Illumina Hiseq 2000 sequencer) for differential gene expression between control and treated samples. I am using CLCBio genomic workbench for the expression analysis. I have mapped the reads using RPKM method. If I am not wrong, I understand that RPKM is a type of normalisation within sample group. But if I need to compare between samples (control vs treated), how should I should normalize to get the differential expression.
I also see one option, log-transformation, before normalization. Do I need to do log-transformation with the RNAseq expression data generated through RPKM method.
Additionally, for RNAseq data which method is better for normalization; scaling, quantile or by total?
Please suggest and share your thought.
I am working on a set of bacterial RNAseq data (generated using Illumina Hiseq 2000 sequencer) for differential gene expression between control and treated samples. I am using CLCBio genomic workbench for the expression analysis. I have mapped the reads using RPKM method. If I am not wrong, I understand that RPKM is a type of normalisation within sample group. But if I need to compare between samples (control vs treated), how should I should normalize to get the differential expression.
I also see one option, log-transformation, before normalization. Do I need to do log-transformation with the RNAseq expression data generated through RPKM method.
Additionally, for RNAseq data which method is better for normalization; scaling, quantile or by total?
Please suggest and share your thought.
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