Thanks for helping to solve this problem. For my final implementation of p.adjust function from R in Perl I need to provide you the entire algorithm. Basically you have solved a lot of it. I do not have any problem with section (d), but based on what I was thinking and you implemented the order that I get at (c) is different from what it should be. </code>

(a) sort these values in an decreasing order

0.9802138 0.9585124 0.8167950 0.6491767 0.5453980 0.4902384 0.4693030 0.4069490 0.2821822 0.1155778

(b) assign order to each above observation in a decreasing order, i.e.,

10 9 8 7 6 5 4 3 2 1

(c) then calculate

0.9802138*10/10 0.9585124*10/9 0.8167950*10/8 ..... 0 .1155778*10/1 (note that: the 10 in the numerator corresponds to the total number of tests conducted in this toy example, you should change this to the corresponding actual number of tests when you do real data analysis. Also the order assignment will start with the total number of tests and decrease to 1.)

You will obtain the following

0.9802138 1.0650138 1.0209938 0.9273953 0.9089967 0.9804768 1.1732575 1.3564967 1.4109110 1.1557780

(d) then do the the cumulative minimum adjustment, i.e.

since 0.9802138<1.0650138, replace 1.0650138 with 0.9802138,

then among the first three values 0.9802138, 0.9802138, 1.0209938, 0.9802138 is smallest, replace 1.0209938 with 0.9802138

then among the first four values 0.9802138, 0.9802138, 0.9802138, 0.9273953, 0.9273953 is the smallest, and the fourth value will not be changed

similarly, the fifth value will not be changed and all the rest of values will be changed to 0.9089967

Finally you should have 0.9802138, 0.9802138, 0.9802138, 0.9273953 0.9089967 0.9089967 0.9089967 0.9089967 0.9089967 0.9089967

rearrange these value according to the original order of p-value,

0.5453980 0.4902384 0.8167950 0.2821822 0.4693030 0.6491767 0.9802138 0.1155778 0.9585124 0.4069490 

[6]      [5]        [8]     [2]      [4]     [7]        [10]     [1]  
+        [9]     [3]

[download]

then you will obtain the following values

0.9089967 0.9089967 0.9802138 0.9089967 0.9089967 0.9273953 0.9802138 0.9089967 0.9802138 0.9089967

then you compare each of these values (in red) with 1, if it is greater than 1, then replace that value with 1. Since in this particular example, all the above values (in red) are less than 1, your final BH adjusted q-values are

0.9089967 0.9089967 0.9802138 0.9089967 0.9089967 0.9273953 0.9802138 0.9089967 0.9802138 0.9089967

In reply to Re^4: Restore the original order of an array after sort and performing some funchtion on array values by sesemin
in thread Restore the original order of an array after sort and performing some funchtion on array values by sesemin

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