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2 votes

How to normalise Bulk RNA-seq data to account for transcript length, coverage depth, library size and batch effects?

All factors you mention bar the batch effects can be addressed by some sort of normalization (I use a modified version of UQpgQ2). Batch effects can be addressed using ComBat/SVA/ComBat-seq but my ...
Ram RS's user avatar
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2 votes
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Inconsistent microarray expression levels after normalizing with log2

As I already told you here (When analysing microarray data, is it need to do normalization and standardization both?) log2 is a transformation, not a normalization so unless these data were already ...
ATpoint's user avatar
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1 vote
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When analysing microarray data, is it need to do normalization and standardization both?

Actually, there is three terms to introduce, which is normalization, transformation and standardization. Normalization corrects for biases such as different baselines of array intensities, or in RNA-...
ATpoint's user avatar
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1 vote

How to normalise Bulk RNA-seq data to account for transcript length, coverage depth, library size and batch effects?

Have a look through the DESeq2 manual. It goes into a lot of detail about how it works, and how you can use it to do all the things you're asking about: https://www.bioconductor.org/packages/devel/...
gringer's user avatar
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