Operators in Color Set Criteria

[Daniel]

I'm trying to compare groups of tumors using an mRNA expression
dataset to find active pathways in different groups but the operators
don't seem to be very intuitive.

I tried comparing two tumors to another one using this code: [1] AND
[2] > [3] thinking that GenMAPP would analyze the data and color the
genes the appropriate color that had higher expression in BOTH 1 and 2
compared to 3. Instead I found that it only compared 2 and 3 (because
I went back to the original expression sheet and double checked what
it was doing).

Next, I tried simply putting parentheses around 1 and 2 so it looked
like this: ([1] AND [2]) > [3]. That seemed to subtract 2 from 1 which
is very confusing. I was able to get it to work using the code: [1] >
[3] AND [2] > [3] but I am going to be comparing much larger groups of
tumors in the near future and I was hoping there was a more efficient
way of writing the code than having to compare every single tumor from
one group to every single tumor in the other group.

Thanks for your help!

Daniel

[Martijn van Iersel]

As far as I know there is no way around this. The final expression you
mention is the only one that will be interpreted correctly.

But if you find yourself writing long expressions like that all the time
GenMAPP, it may be easier to prepare the data in Excel before importing.
For example, assuming [1] is in column A, [2] in column B etc.:

=if (A2>C2 AND B2>C2,1,0)

And then in GenMAPP you can use the code "[4] = 1"

Excel uses the same logic as GenMAPP for evaluating expressions, so that
won't be easier, but in Excel it may be quicker to try out different
formula's or copy / paste them.

hope this helps,
Martijn