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We need to plot the sizes of dna fragments using a log10 base pairs on the y axis. The problem is I have no idea what any of this means. Where do I even start? I tried looking up videos and found some very simplified versions. Then some girl on my course started talking about using "antilogs" and I am extremely confused. If someone could give me a simple introduction to log scales I'd really appreciate it!
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Meowstic
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if you had y axis values between 0.0001 and 1000000 it wouldn't really make sense to plot them on a linear scale so sometimes a logarithmic scale is used. The only thing you need to do is do log(y) for each value and plot those instead. log should be base 10 by default on a calculator but there will be a button that lets you choose the base
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Anonymous #1
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(Original post by Meowstic)
if you had y axis values between 0.0001 and 1000000 it wouldn't really make sense to plot them on a linear scale so sometimes a logarithmic scale is used. The only thing you need to do is do log(y) for each value and plot those instead. log should be base 10 by default on a calculator but there will be a button that lets you choose the base
So I’d have a regular scale on the y axis. And for each “result” that I have (in this case, size of DNA fragments), I would just stick that value into my calculator and plot whatever I get? Where do “anti logs” come into this because apparently I’m supposed to use it.... :\

Thank you by the way!
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Meowstic
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(Original post by Anonymous)
So I’d have a regular scale on the y axis. And for each “result” that I have (in this case, size of DNA fragments), I would just stick that value into my calculator and plot whatever I get? Where do “anti logs” come into this because apparently I’m supposed to use it.... :\

Thank you by the way!
it's the inverse of a logarithm. as you are a sane person you will know it as exponentiation and not 'anti-logging'. 10^a = b <=> log(b) = a
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simon0
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To add to Meowstic's posts, the log (to the base 10) of a value is simply the power of 10 to get that value, for example:

 \log _{10} (100) = 2 since  10^{2} = 100,

so the log of 100 is 2 since you need to 10 squared to get 100.

This is done since the values you have may cover a wide range so it is more practical to use logs of those values instead (so using the example above instead of plotting 0.0001 and 1000000, we can plot instead:

-4, (which is  \log _{10} (0.0001), since  10^{-4} = 0.0001 ),

6, (which is  \log _{10} (1000000), since  10^{6} = 1000000 )).

Is that more clear?
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mnot
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(Original post by Anonymous)
We need to plot the sizes of dna fragments using a log10 base pairs on the y axis. The problem is I have no idea what any of this means. Where do I even start? I tried looking up videos and found some very simplified versions. Then some girl on my course started talking about using "antilogs" and I am extremely confused. If someone could give me a simple introduction to log scales I'd really appreciate it!
antilog, my new favourite terminology, perhaps these girls are also confused and mean exponential (I dont know why but I found that very funny).

Meowstic & simon0 hopefully have cleared up what's actually happening in a log scaled graph.
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Snfkin
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Thanks guys! That really helped! To clear things up, say if I had a DNA fragment with a size of 4000 base pairs and it moved 20mm down the gel electrophoresis paper, would I just stick the 4000 into my calculator log function and plot that result (3.602...) on the y axis, against the distance on the x axis (so 20mm in this case)?
But when I look up log paper on google, it seems that the y axis scales are all really large, like 100-1000 intervals, so how am I supposed to plot the 3.602?
And still not sure where "exponential" comes in as I've just discovered that I do indeed have to use it. Somehow...?
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Snfkin
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Name:  DNA.png
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This is an example we were given, it's apparently a semi log graph but I have no idea how. Because if it was, shouldn't the y-axis be non-linear? Sorry the pic is so small and bad quality, it is like that for me too lol, but along the y axis the intervals are 100, 1000 and 10000. Distance along the bottom. Also, as mentioned above the values are really big. That's like if I just didn't use log at all....?
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simon0
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Biology is not my speciality but judging by your uploaded image and searching for DNA base pair gel electrophoresis semi-log graphs, I am guessing the y-axis is logarithmic but the y-axis labels are the actual numbers rather than the equivalent log value of the actual value.

(Note on the y-axis, as you go up at every set interval the label is 10 times bigger than the previous value below).

Am I correct in this?
(If not then post away).
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Snfkin
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(Original post by simon0)
Biology is not my speciality but judging by your uploaded image and searching for DNA base pair gel electrophoresis semi-log graphs, I am guessing the y-axis is logarithmic but the y-axis labels are the actual numbers rather than the equivalent log value of the actual value.

(Note on the y-axis, as you go up at every set interval the label is 10 times bigger than the previous value below).

Am I correct in this?
(If not then post away).
I think so? Pls note that I'm really, really dense and also confused so I'm not too clear myself :confused:
But yeah seems like the y axis is logarithmic (if my definition of logarithmic as meaning an axis' intervals goes up/down irregularly is correct), but then the next issue is .... why do I have to use the log function if the intervals are as you said, the actual numbers? If it helps, I am supposed to be making a "semi-log graph."

Also, I still have no idea where the exponential is supposed to come in, how I'm supposed to use it etc.....
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simon0
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No problems.

The y-axis is still logarithmic but the individual labels have been replaced by the actual values rather than their log values (it is still a semi-log graph but the only difference is the y-axis labels e.g. Instead of label "3", they use label "1000").

Is that better?
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Snfkin
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(Original post by simon0)
No problems.

The y-axis is still logarithmic but the individual labels have been replaced by the actual values rather than their log values (it is still a semi-log graph but the only difference is the y-axis labels e.g. Instead of label "3", they use label "1000").

Is that better?
It is! Thank you for your help! So basically, I don’t have to use the log function on my calculator at all?
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simon0
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(Original post by Snfkin)
It is! Thank you for your help! So basically, I don’t have to use the log function on my calculator at all?
You do need to use the log function since you are plotting distance against log of the base pairs!

The only change are just the y-axis labels.
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simon0
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What I suggest is plot distance (x-axis) against the log of the base pairs (y-axis) and plot all those points.

Then after, change the y-axis labels to their normal numbers (so "2" goes to "100", "3" goes to "1000" etc.).
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Snfkin
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(Original post by simon0)
What I suggest is plot distance (x-axis) against the log of the base pairs (y-axis) and plot all those points.

Then after, change the y-axis labels to their normal numbers (so "2" goes to "100", "3" goes to "1000" etc.).
Thank you so much Just finished my graph
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simon0
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(Original post by Snfkin)
Thank you so much Just finished my graph
Great, the method I mentioned was based on my judgment but I have no experience in this myself so there may be some details I may have missed out.

However, does your graph look fine or can it be confirmed to be done correctly?
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