[BioC] A question related to converting p values to -log p

[James W. MacDonald]

Did you try -log(p)?

This should work provided the zeros you report below aren't really zero.

Best,

Jim



Li, Aiguo (NIH/NCI) [C] wrote:
> Dear all,
> 
>  
> 
> I have a list of p values as below and would like to convert it into
> minus log p.  How should I do it in R?
> 
>  
> 
> Thanks in advance,
> 
>  
> 
> AG Lee
> 
>  
> 
> 0
> 
> 0.069805
> 
> 0
> 
> 0
> 
> 0
> 
> 0
> 
> 0
> 
> 0
> 
> 0
> 
> 0.176752
> 
> 0.049759
> 
> 0.143271
> 
> 0.122581
> 
> 0.012448
> 
> 0.037795
> 
> 0
> 
> 0.004878
> 
> 0.319481
> 
> 0.07681
> 
> 0.106322
> 
> 0.005626
> 
> 0.852804
> 
> 0.011966
> 
> 0.197347
> 
> 0.081081
> 
> 0.809278
> 
> 0.012658
> 
> 0.190164
> 
> 0.010417
> 
> 0.242424
> 
> 0.003454
> 
> 0.211268
> 
> 0.257426
> 
> 0.287611
> 
> 0.455696
> 
> 0
> 
> 0.822715
> 
> 0.692568
> 
> 0.141827
> 
> 0.053435
> 
> 0.211744
> 
> 0.002809
> 
> 0
> 
> 0.897356
> 
> 0.052373
> 
> 0.077544
> 
> 0.015652
> 
> 0
> 
> 0.115321
> 
> 0.415888
> 
> 0
> 
> 0.854914
> 
> 0
> 
> 0.173913
> 
> 0.926509
> 
> 0.007704
> 
> 0.144578
> 
> 0.071186
> 
> 0
> 
> 0.343849
> 
> 0.545757
> 
> 0
> 
> 0.09913
> 
> 0.056106
> 
> 0.088586
> 
> 0.942356
> 
> 0.249117
> 
> 0
> 
> 0.438356
> 
> 0.673736
> 
> 0.017857
> 
> 0.22973
> 
> 0.203306
> 
> 0.027553
> 
> 0.872822
> 
> 0.387987
> 
> 0.11324
> 
> 0.033762
> 
> 0.106796
> 
> 0.219585
> 
> 0
> 
> 0.365052
> 
> 0.03405
> 
> 0.261111
> 
> 0.913559
> 
> 0.017945
> 
> 0.004951
> 
> 0
> 
> 0.015038
> 
> 0.066884
> 
> 0.138748
> 
> 0.213287
> 
> 0.01071
> 
> 0.028668
> 
> 0.115587
> 
> 0.830846
> 
> 0.015152
> 
> 0.71
> 
> 0
> 
> 0.060606
> 
> 0.190554
> 
> 0.156627
> 
> 0.00821
> 
> 0.031949
> 
> 0.866005
> 
> 0.00361
> 
> 0.008562
> 
> 0.340836
> 
> 0.02916
> 
> 0.46677
> 
> 0.328205
> 
> 0.049404
> 
> 0.588618
> 
> 0.008902
> 
> 0.614238
> 
> 0.612795
> 
> 0.155673
> 
> 0.003077
> 
> 0.633157
> 
> 0.685864
> 
> 0.54321
> 
> 0.015437
> 
> 0.014085
> 
> 0.983452
> 
> 0
> 
> 0.72758
> 
> 0.407718
> 
> 0.153199
> 
> 0.528875
> 
> 0.563679
> 
> 0
> 
> 0.056899
> 
> 0.073552
> 
> 0.476271
> 
> 0.126904
> 
> 0.003115
> 
> 0.268608
> 
> 0.571207
> 
> 0.02139
> 
> 0.135987
> 
> 0.037705
> 
> 0.005076
> 
> 0.017268
> 
> 0.269663
> 
> 0.00846
> 
> 0.095638
> 
> 0.00624
> 
> 0.817708
> 
> 0.801038
> 
> 0.343333
> 
> 0.641538
> 
> 0
> 
> 0.011349
> 
> 0.005181
> 
> 0.098361
> 
> 0.048991
> 
> 0.017301
> 
> 0.306733
> 
> 0.222222
> 
> 0.327243
> 
> 0.001504
> 
> 0.004666
> 
> 0.015912
> 
> 0
> 
> 0.312
> 
> 0.046823
> 
> 0.076299
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623