Question

micro-array analysis without FoldChange

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5.7 years ago

Morteza Hadizadeh ▴ 60

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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ADD COMMENT • link updated 5.7 years ago by Benn 8.3k • written 5.7 years ago by Morteza Hadizadeh ▴ 60

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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.

ADD REPLY • link 5.7 years ago by ATpoint 81k

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Thank you for taking this into consideration.

ADD REPLY • link 5.7 years ago by Morteza Hadizadeh ▴ 60

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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.

ADD REPLY • link 5.7 years ago by Benn 8.3k

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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?

ADD REPLY • link 5.7 years ago by Morteza Hadizadeh ▴ 60

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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.

ADD REPLY • link 5.7 years ago by Arup Ghosh 3.2k

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

ADD REPLY • link 5.7 years ago by Antonio R. Franco ★ 5.1k

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moderated F-statistic, check ?topTable https://www.rdocumentation.org/packages/limma/versions/3.28.14/topics/toptable

ADD REPLY • link 5.7 years ago by Benn 8.3k

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No, F means F-statistic or Fisher statistic

ADD REPLY • link 5.7 years ago by Morteza Hadizadeh ▴ 60

score 0 · Answer 1 · 2018-07-27

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!