based on multiple simultaneous tests p-values
compute_q_values.pl $inputFile1 $inputLambda2 $inputPI0_method3 $inputFDR_level4 $inputRobust5 $outputFile1 $outputFile2
.. class:: infomark
**What it does**
This program computes the q-values based on the p-values of multiple simultaneous tests. The q-values are computed using a specific R package, created by John Storey and Alan Dabney, called "qvalue". The program takes five inputs:
- The first input is a TABULAR format file consisting of one column only that represents the p-values of multiple simultaneous tests, one line for every p-value.
- The second input is the lambda parameter. The user can choose either the default: seq(0, 0.95, 0.05) or a decimal number between 0.0 and 1.0.
- The third input is PI method which is either "smoother" or "bootstrap".
- The fourth input is the FDR (false discovery rate) level which is a decimal number between 0.0 and 1.0.
- The fifth input is either TRUE or FALSE for the estimate robustness.
The program gives two outputs:
- The first output is a TABULAR format file consisting of three columns:
- the left column represents the p-values of multiple simultaneous tests, one line for every p-value
- the middle column represents the q-values corresponding to the p-values
- the third column represent the significance values, either 1 for significant or 0 for non-significant
- The second output is a PDF format file consisting of three pages:
- the first page represents the p-values histogram
- the second page represents the q-values histogram
- the third page represents the four Q-plots as introduced in the "qvalue" package manual.
**Example**
Let us have the first input file of p-values as follows::
0.140627492
0.432249886
0.122120877
0.142010182
0.012909858
0.000142807
0.039841941
0.035173303
0.011340057
1.01E-05
0.212738282
0.091256284
0.547375415
0.189589833
6.18E-12
0.001235875
1.10E-05
9.75E-07
2.13E-18
2.54E-16
1.20E-19
9.76E-14
0.359181534
0.03661672
0.400459987
0.387436466
0.342075061
0.904129283
0.031152635
Running the program will give the following output::
pi0: 0.140311054
FDR level: 0.05
p-value q-value significant
0.1406275 0.02889212 1
0.4322499 0.06514199 0
0.1221209 0.02760624 1
0.1420102 0.02889212 1
0.01290986 0.00437754 1
0.000142807 6.46E-05 1
0.03984194 0.01013235 1
0.0351733 0.009932946 1
0.01134006 0.004194811 1
1.01E-05 5.59E-06 1
0.2127383 0.03934711 1
0.09125628 0.02184257 1
0.5473754 0.07954578 0
0.1895898 0.03673547 1
6.18E-12 5.03E-12 1
0.001235875 0.00050288 1
1.10E-05 5.59E-06 1
9.75E-07 6.61E-07 1
2.13E-18 4.33E-18 1
2.54E-16 3.45E-16 1
1.20E-19 4.88E-19 1
9.76E-14 9.93E-14 1
0.3591815 0.06089654 0
0.03661672 0.009932946 1
0.40046 0.0626723 0
0.3874365 0.0626723 0
0.3420751 0.06051785 0
0.9041293 0.1268593 0
0.03115264 0.009750824 1
.. image:: ../static/operation_icons/p_hist.png
.. image:: ../static/operation_icons/q_hist.png
.. image:: ../static/operation_icons/Q_plots.png