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

[Morten Mattingsdal]

Hi,

Paste the following code, and the -log values is in the object 
"logged"... paste all the below code:

AGLee <- scan(nlines=167,what=list(0))
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


aglee=as.data.frame(AGLee)
logged=-log(aglee)
print("Bioconductor is King")



> 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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