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micro-array analysis without FoldChange

Hi everyone

Why do some microarray analysis without FoldChange (in the top table)? How to extract up and down-regulated genes (with adj.P.Val and lack of FC)?

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• 2,418 views • link
updated by Benn Benn • written by Morteza Hadizadeh • Morteza Hadizadeh

I edited your question to correctly display the picture. For the future, please make sure that you add a link with a valid suffix, like .png or .jpg. Also see How to add images to a biostars post.

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written by ATpoint ATpoint

Why do you lack FC? What code did you use? Explain where you got this incomplete table, or what you have done to get this table. Now your question contains not enough info.

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written by Benn Benn

The table is complete, F-statistic is used for comparing more than two groups. My question is that how to extract significant genes without FC? or Is "adj.P.Val" sufficient for analysis alone?

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written by Morteza Hadizadeh • Morteza Hadizadeh

if you have the data reanalyze it. Without the fold change you can't extract "up or down-regulated" genes, as both up and down-regulated genes can have the same level of significance.

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written by Arup Ghosh Arup Ghosh

what is the meaning of the "F" column ?. Can it stands for "Fold" ?

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written by Antonio R. Franco Antonio R. Franco

1 answer

I don't know where you got this table from, and you don't seem to want to give more info. So here the explanation. The topTable was made without a defined contrast. Why?, you should ask the makers of this table. How to get the FC? Make a contrast first, before generating the topTable. Good luck!

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written by Benn Benn

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