Question

heatmap-gene expression

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2.9 years ago

Bioinformatics1 ▴ 10

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 • 1.2k views

ADD COMMENT • link updated 2.7 years ago by seidel 11k • written 2.9 years ago by Bioinformatics1 ▴ 10

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please, take a moment to fill a real list of tags.

ADD REPLY • link 2.9 years ago by Pierre Lindenbaum 164k

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

ADD REPLY • link 2.9 years ago by Bioinformatics1 ▴ 10

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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

ADD REPLY • link 2.9 years ago by GenoMax 148k

score 2 · Answer 1 · 2022-01-16

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.