I want to present my differential expression data as log ratio instead of just giving fold change I thought I could use log2 change but the - overall - value (down regulation) gives me error. Any suggestion what should be the best way to present log ratio of differential expression. To further clarify I have expression of A - expression of B = differential expression C and transfer to log ratio of C
Thanks
Dear,
Negative values will throw an error. you cannot get a negative value for 2^b whatever real number you give to b. Try to do this:
log[1+|C|/min(A,B)]*sign(A-B)
where |C| is the absolute value of C, and min(A,B) is the smallest of A and B, and sign(A-B) is just the sign. Change the (A-B) to (B-A) if you plot B on top or vice versa.
I hope it helps,
Regards,
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written
by
Ibrahim Tanyalcin
Let em explain little more about my challenge. I have list of genes which are mostly upregulated except 3-4 genes which are down regulated. I want to send this table as supplementary table for publication and want to use instead of absolute fold change. I have seen several paper publications listing log ratio.
Here is an example of one such paper.
Any suggestion what should be the best way to present log ratio of differential expression.
Yes, present differential expression as a log2 ratio. If A = 32 and B = 18, the A/B ratio is 32/18 = 1.77. The log2(1.77) = 0.83. (what is the exact nature of the error you get?). To retrieve the original linear ratio value: 2^0.83 = 1.77. It all works the same even if the ratio was the other way around B/A = 18/32 = 0.56; and log2(0.56) = -0.83; and 2^-0.83 = 0.56. And if your numbers are starting off in log space (since you have A - B depicting a ratio), then C is already a log value and does not need to transformed to log space.
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