Hello - I am a genetics researcher. I have a series of data points with errors (standard errors), that I wish to plot as a graph plot:
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
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