GENE, AVG FOLD CHANGE, SE

Gene1, 2193.10, 1200.74

Gene2, 96.28, 9.08

Gene3, 39.02, 22.51

Gene4, 5.88, 0.82

Gene5, -0.68, 0.33

Gene6, 1.14, 0.02

Gene7, -1.46, 0.16

Gene8, -1.56, 0.50

Gene9, -1.58, 0.10

Gene10, -1.88, 0.45

Gene11, -2.04, 0.45

Gene12, -6828.82, 975.41

Positive values are up-regulated genes; negative values are down-regulated genes (re: gene expression levels).

I wish to plot this as a column plot on a log scale (y-axis) with negative values below the zero baseline, positive values above, and with the errors indicated.

Something like:

1000

100

10 *

1 *

0-------------------

-1 *

-10 *

-100

-1000

but with bars instead of the asterisks - you get the idea. I can do this easily enough using MS Excel, by taking the log of the absolute value, multiplying the result by +1 or -1 (to restore the original "directionality" - i.e. up- or down-regulated).

A couple of questions:

(Q1) Is it "better" to use log (base 10) or ln (natural) log transformations?

(Q2) How would I present the error bars - would I log (or ln) -transform the standard errors, for example, and plot these [or the absolute values of these, since the log of numbers <1 are negative; e.g. log(0.5) = -0.301)]?

I tried finding the answer to these questions in Google, but I wasn't very successful. ...

I would very much appreciate any comments regarding the log-transformation of data and plots of log-transformed data, particularly regarding error bars!

Thank you!

Sincerely,

Greg