heatmap-gene expression
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4 months ago

I used pipeline R for analyzing gene expression. The pipeline was for 500 genes. The person who reviewed my paper asked why did I choose 500 genes to draw a heatmap and analyze gene expression.

What can be the answer? because if fold change? Thanks,

genes heatmap expression • 479 views
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please, take a moment to fill a real list of tags.

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Please show me the instruction. I don't understand.

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Edit your original post. Then fix the list of words so they actually reflect the question content (circled). You are allowed a maximum of 5 so choose the words carefully. e.g. heatmap, gene_expression, fold_change can be good examples.

fix tags

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4 months ago

Well, why did you use 500 genes? How are we supposed to answer that for you? If it's arbitrary, you may as well state as much. Presumably, it's the top 500 based on effect size rather than significance, I'd hope. You may need to re-analyze with a defined threshold for log fold change or such to have a real answer, though you should really perform DE with such thresholds as your null hypothesis rather than filtering post hoc.

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