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Z score and FC

I have results of expression as Fold change and Z score. The Z score is a negative value while FC is >1.2. I was wondering what should be used FC or Z score. I understand that z score is the deviation from mean value and can be plus or minus.

rna-seq
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written by kanwarjag kanwarjag

1 answer

How were these results produced? It is possible to have a variable with negative Z-score, coupled with a positive fold-change. You could go by |Z| = 1.96 as a cut-off for statistical significance.

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written by Kevin Blighe Kevin Blighe

You are right I have large negative z score with positive FC. How do I calculate |Z| , I googled it but could not find. So what should be considered FC

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written by kanwarjag kanwarjag

|Z| refers to the absolute value of Z. What I mean is, in the absence of any p-values, explore the following as your cut-offs:

  • Z > 1.96 & FC > 2
  • Z > 1.96 & FC < -2
  • Z < -1.96 & FC > 2
  • Z < -1.96 & FC < -2

You did not answer my question about how the data was processed, so, I cannot help you further. It is interesting and surprising that you have been presented with data that has no p-values.

Also be weary of whether or not your 'FC' values are linear, natural log, or log [base 2] fold changes.

Good luck.

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written by Kevin Blighe Kevin Blighe

My apology- P values are there raw p values looks good <0.01 That is the reason I could not grasp what is happening and what to use. Again thanks

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written by kanwarjag kanwarjag

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