[BioC] delta table interpretation in samr package
Xiang [guest]
guest at bioconductor.org
Mon May 27 22:15:15 CEST 2013
Hi, there,
I'm trying to identify differentially expressed genes after treatment using two class paired option of samr function.
samr.obj<-samr(samData, resp.type="Two class paired", nperms=100)
delta.table<-samr.compute.delta.table(samr.obj, min.foldchange=1.5)
The median FDR rate is 0 for all 50 delta values. The number of called genes remains to be 368 when delta value changes from 0 to 1.09.
Could anyone let me know if it's OK to use 0 as delta value for samr.compute.siggenes.table? I don't understand why FDR is 0 for delta of 0. Isn't FDR suppose to be 1 if the cutoff value is 0?
thanks a lot
Xiang
-- output of sessionInfo():
delta # med false pos 90th perc false pos # called median FDR 90th perc FDR cutlo cuthi
[1,] 0.000000000 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[2,] 0.001390547 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[3,] 0.005562188 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[4,] 0.012514923 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[5,] 0.022248752 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[6,] 0.034763676 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[7,] 0.050059693 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[8,] 0.068136804 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[9,] 0.088995010 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[10,] 0.112634309 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[11,] 0.139054703 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[12,] 0.168256191 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[13,] 0.200238772 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[14,] 0.235002448 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[15,] 0.272547218 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[16,] 0.312873082 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[17,] 0.355980039 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[18,] 0.401868091 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[19,] 0.450537237 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[20,] 0.501987477 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[21,] 0.556218812 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[22,] 0.613231240 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[23,] 0.673024762 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[24,] 0.735599378 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[25,] 0.800955089 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[26,] 0.869091893 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[27,] 0.940009792 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[28,] 1.013708784 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[29,] 1.090188871 0 3.9241377 368 0 0.010663418 -2.018916e+00 2.311858e+00
[30,] 1.169450051 0 3.5317239 366 0 0.009649519 -2.018916e+00 2.427889e+00
[31,] 1.251492326 0 3.0957086 365 0 0.008481393 -2.018916e+00 2.648676e+00
[32,] 1.336315695 0 1.3080459 363 0 0.003603432 -2.449141e+00 2.917082e+00
[33,] 1.423920158 0 0.9156321 358 0 0.002557632 -2.449141e+00 3.162520e+00
[34,] 1.514305715 0 0.4796168 354 0 0.001354850 -2.449141e+00 3.542451e+00
[35,] 1.607472366 0 0.4360153 349 0 0.001249327 -2.610891e+00 3.651504e+00
[36,] 1.703420111 0 0.4360153 344 0 0.001267486 -2.888436e+00 3.963871e+00
[37,] 1.802148950 0 0.0000000 340 0 0.000000000 -2.888436e+00 4.458064e+00
[38,] 1.903658883 0 0.0000000 335 0 0.000000000 -3.045751e+00 4.458064e+00
[39,] 2.007949910 0 0.0000000 327 0 0.000000000 -3.180299e+00 4.516839e+00
[40,] 2.115022031 0 0.0000000 317 0 0.000000000 -3.351132e+00 4.819126e+00
[41,] 2.224875247 0 0.0000000 306 0 0.000000000 -3.547589e+00 4.873843e+00
[42,] 2.337509556 0 0.0000000 288 0 0.000000000 -3.754290e+00 5.592262e+00
[43,] 2.452924959 0 0.0000000 261 0 0.000000000 -3.953790e+00 5.592262e+00
[44,] 2.571121457 0 0.0000000 222 0 0.000000000 -4.185488e+00 5.592262e+00
[45,] 2.692099048 0 0.0000000 145 0 0.000000000 -4.499563e+00 5.592262e+00
[46,] 2.815857734 0 0.0000000 64 0 0.000000000 -4.875999e+00 1.000000e+10
[47,] 2.942397514 0 0.0000000 31 0 0.000000000 -5.176429e+00 1.000000e+10
[48,] 3.071718387 0 0.0000000 21 0 0.000000000 -5.400854e+00 1.000000e+10
[49,] 3.203820355 0 0.0000000 2 0 0.000000000 -6.214298e+00 1.000000e+10
[50,] 3.338703417 0 0.0000000 0 NaN NaN -1.000000e+10 1.000000e+10
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