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Re: [GeneX-dev] CyberT bug
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From: Michael P. <mic...@ho...> - 2001-02-02 21:11:12
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Ok, time to answer my own question.. "lnp" means "p of ln() tranformed data" according to the documentation.... that's right I didn't read it first. Suggestion: all of the "ln" columns might be better expressed as "p(ln)", "t(ln)" etc. as a way to distinguish. "lnp" is just too similar to ln(p) to not make the leap. Regards, Michael Pear ----- Original Message ----- From: "Michael Pear" <mic...@ho...> To: "Harry Mangalam" <man...@ho...> Cc: <gen...@li...> Sent: Friday, February 02, 2001 1:03 PM Subject: Re: [GeneX-dev] CyberT bug > Harry, > I notice that the "lnp" column doesn't seem to be the natural logarithm of > the "p"... When I plot lnp vs. p in xgobi, I get a scatter plot rather than a clear > functional relationship and even when p<1, displayed values for lnp are positive. > Am I missing something? > > Regards, > > Michael Pear > ----- Original Message ----- > From: "Harry Mangalam" <man...@ho...> > To: <td...@ho...> > Cc: "genexdev at SF" <gen...@li...> > Sent: Friday, February 02, 2001 11:28 AM > Subject: [GeneX-dev] CyberT bug > > > > Hi Tony, > > > > I think there is a bug in the CyberT interface (or R code). Michael Pear, who has been stress > testing the whole of GeneX is generating C+E data that he has loaded into his GeneX database and > trying > > to analyze it via the CyberT C+E tool. > > > > He found that > > ===> > > 2) There appears to be a "minrep" level set to 2 when calling "doitall" that > > is to prevent t-testing on too small a number of replicates. However, it seems that there is still > a "p" value and fold computed for spots that violate this minimum requirement...am I missing > > something? We are finding the some of our best "p" values are for spots that do not satisfy the > "minrep" requirement. > > <=== > > > > Have I gotten this right below? And if so, there is a mismatch between what I understand to be > happening and what the doitall script is doing. Is my suggestion below the correct approach or is > there > > a deeper bit that I'm missing? > > > > I've partially tracked it down to bad/misleading documentation at minimum. > > > > The values that he's trying to analyze have negative #s in them. He currently has the option of > indicating that they are either below backgound (in which case they are set to 0) > > > > That's what this means in the C+E form: > > == > > Values less than [ ] will be set to 0 and ignored in calculations. (Leave blank to include all > values). > > == > > It turns out that it's actually NOT ignored in calculations. It's USED in the calculations AS > ZERO, as ZERO is a valid number for this calculation. I think the interface should allow you to set > the > > number to the cutoff (or even another number) or to set it to 'NA' (which indicates a true missing > value - see below) > > > > However, you CAN tell the program to IGNORE the values by setting negative values to 'NA' (as is > described in the help, but that's off the main page). That results in what you would expect for the > > above case. This is also reasonably easy to fix, so that the above FORM widget should be > rephrased as: > > > > == > > Leave the following value blank to include all values. > > Values less than [___] will be set to > > <> that value and included in calculations as that vlaue > > <> NA and ignored in further calculations. > > > > where <> is a radio-type button. > > == > > This should also be available from both the DB data entry and the upload data entry. > > > > > > > > Thanks > > hjm > > > > > > Harry Mangalam wrote: > > > > > > Hi Michael, > > > > > > Is this from data passed in directly from a database query? or did you upload it from a file. > The difference is that if it comes in from the DB, some variables are already set (the minrep param > is > > > one of them I think). > > > > > > However the fact that minrep is getting set to 2 and that's getting passed to doitall is weird. > I'm checking now.. > > > > > > And attached to this is the replacement 'dendro.jar' file that may fix your applet problem. > (actually this has been deleted b/c of the size restriction on the list - I sent it and then I as > admin got > > > the request to approve it... proving the point that idiots rule!) > > > > > > hjm > > > > > > Michael Pear wrote: > > > > > > > > > > 2) There appears to be a "minrep" level set to 2 when calling "doitall" that is to prevent > > > > t-testing on too > > > > > > small a number of replicates. However, it seems that there is still a "p" value and fold > > > > computed for spots > > > > > > that violate this minimum requirement...am I missing something? We are finding the some of > our > > > > best > > > > > > "p" values are for spots that do not satisfy the "minrep" requirement. > > > > > > > > > > Hmm - that shouldn't be the case - it should refuse to calculate these. No wonder that > they're > > > > the best p's are with these - they'd tend to have less variability. This is with the C+E > cybert? > > > > > > > > Yes, this is with C+E cybert. I have attached a snippet from the output of one of the runs. > > > > See, for example, the line "125", which gives a p value of ~.08, but has only one replicate > from the > > > > control set. > > > > > > > > Michael Pear > > > > > > > > > > -- > > Cheers, > > Harry > > > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho... > > > -------------------------------------------------------------------------------- > > > > R version R 1.2.1 (2001-01-15). > > Cyber-T version 6.2C+E > > hdarray library version 3.5 > > Date of this analysis (YYYY-MM-DD) was 2001-02-01 > > > > Row# "Lab_0" "C_1" "C_2" "C_3" "E_4" "E_5" "E_6" "C#obs" "E#obs" "C.Mn" "E.Mn" "C.SD" "E.SD" > "ClnMn" "ElnMn" "ClnSD" "ElnSD" "t" "t.df" "t.var" "lnt" "lnt.df" "lnt.var" "p" "lnp" "fold" > > "1" "E06a" 5576 760 7256 2960 6640 208 3 3 4530.66667 3269.3333 3371.801497 3227.138258 > 8.049710 7.377117 1.23367848 1.811931358 -0.468087469 4 1.091664e+00 -0.531451529 4 2.157146e+00 > 0.6640889197 0.6232484745 -1.385808 > > "2" "A06l" 1356 1112 4660 2336 1332 1460 3 3 2376.00000 1709.3333 1981.760833 546.469883 > 7.557660 7.412275 0.77635473 0.301356647 -0.561699930 4 1.315134e+01 -0.302373474 4 6.636802e+00 > 0.6043010773 0.7774383745 -1.390016 > > "3" "A09l" 2324 3448 7748 6672 2652 3428 3 3 4506.66667 4250.6667 2862.782795 2132.530266 8.283928 > 8.276159 0.61388331 0.476192638 -0.124211301 4 1.802131e+00 -0.017319955 4 1.661905e+00 0.9071397521 > 0.9870108454 -1.060226 > > "4" "A03b" 5208 2520 7256 4428 8592 4780 3 3 4994.66667 5933.3333 2375.196273 2309.189757 8.426516 > 8.642162 0.54089721 0.362656878 0.490784928 4 1.057986e+00 0.573552423 4 2.224527e+00 > 0.6492853349 0.5969769219 1.187934 > > ....deleted by mrp.... from 5 to 117........ > > "118" "F03d" 2160 1000 3028 1272 1396 392 3 3 2062.66667 1020.0000 1017.497584 547.386518 > 7.533759 6.786991 0.56783494 0.707971826 -1.563062449 4 3.455243e+00 -1.425188057 4 1.554489e+00 > 0.1930757537 0.2272320109 -2.022222 > > "119" "F10h" 1632 528 2760 1332 1044 0 3 2 1640.00000 1188.0000 1116.021505 203.646753 > 7.196548 7.072626 0.84506959 0.172266827 -0.538910534 3 3.003241e+01 -0.194727236 3 2.406477e+01 > 0.6273715995 0.8580476335 -1.380471 > > "120" "F04h" 5392 3824 2812 1384 11768 7740 3 3 4009.33333 6964.0000 1299.946666 5235.312407 > 8.261125 8.520010 0.32567807 1.134326860 0.948713071 4 1.621938e+01 0.379952063 4 1.213108e+01 > 0.3964880135 0.7232937678 1.736947 > > "121" "E09c" 148 0 216 500 0 0 2 1 182.00000 500.0000 48.083261 NA > 5.186245 6.214608 0.26733313 NA 9.352941200 1 NA 5.440122224 1 NA 0.0678086626 0.1157311046 > 2.747253 > > "122" "A01a" 268 608 1184 1260 1652 2436 3 3 686.66667 1782.6667 463.039235 598.789891 > 6.359272 7.448907 0.74414032 0.331363300 2.507904893 4 1.672297e+00 2.316893154 4 5.043138e+00 > 0.0662052301 0.0814137514 2.596117 > > "123" "E08b" 140 0 0 0 0 0 1 0 140.00000 NA NA NA 4.941642 NA NA NA NA NA > NA NA NA NA NA NA -4.555358 > > "124" "C13d" 720 0 328 336 2132 2524 2 3 524.00000 1664.0000 277.185858 1166.663619 > 6.186132 7.105176 0.55595394 1.118684399 1.292860150 3 1.771533e+01 1.039873073 3 4.048905e+00 > 0.2866235380 0.3748412897 3.175573 > > "125" "C05c" 0 0 140 648 1764 1928 1 3 140.00000 1446.6667 NA 696.509392 4.941642 > 7.171156 NA 0.605483351 3.249364817 2 NA 6.377766652 2 NA 0.0830792373 0.0237135922 10.333333 > > "126" "C06c" 64 0 192 712 1796 2016 2 3 128.00000 1508.0000 90.509668 698.077360 > 4.708189 7.223422 0.77683620 0.570477855 2.641157058 3 5.948633e+01 4.261059559 3 1.854306e+00 > 0.0775789836 0.0237069214 11.781250 > > "127" "C12d" 0 0 148 0 1600 2588 1 2 148.00000 2094.0000 NA 698.621500 4.997212 > 7.618200 NA 0.340034745 3.939271254 1 NA 10.900758910 1 NA 0.1582654014 0.0582384116 14.148649 > > "128" "C03d" 1320 88 252 1020 2176 1664 3 3 553.33333 1620.0000 668.997260 579.254694 > 5.730718 7.343260 1.36520027 0.384184592 2.087769692 4 1.333858e+00 1.969362771 4 1.262737e+01 > 0.1050953318 0.1202572649 2.927711 > > "129" "C01c" 1304 40 196 636 2404 2024 3 3 513.33333 1688.0000 689.165679 930.659981 > 5.380062 7.284306 1.74439186 0.723163700 1.756905339 4 1.823622e+00 1.746628529 4 5.818551e+00 > 0.1537712858 0.1556279159 3.288312 > > "130" "E09d" 448 0 480 400 0 0 2 1 464.00000 400.0000 22.627417 NA > 6.139290 5.991465 0.04878533 NA -4.000000000 1 NA -4.285225084 1 NA 0.1559582608 > 0.1459496634 -1.160000 > > "131" "A04n" 208 0 0 956 0 1092 1 2 208.00000 1024.0000 NA 96.166522 5.337538 > 6.929262 NA 0.094051031 12.000000030 1 NA 23.934215759 1 NA 0.0529293520 0.0265832699 4.923077 > > "132" "C03c" 328 176 1144 1452 1724 1996 3 3 549.33333 1724.0000 520.574042 272.000000 > 6.001928 7.444000 0.95322859 0.159267948 3.463996747 4 3.662918e+00 2.584470449 4 3.582097e+01 > 0.0257238787 0.0610387862 3.138350 > > "133" "C09c" 196 48 0 0 1500 1536 2 2 122.00000 1518.0000 104.651804 25.455844 > 4.574658 7.325079 0.99483818 0.016770117 18.330377969 2 1.690123e+01 3.909309297 2 3.519109e+03 > 0.0029629453 0.0596397842 12.442623 > > "134" "C08c" 80 0 336 308 1992 2512 2 3 208.00000 1604.0000 181.019336 1152.090274 > 5.099569 7.051943 1.01475800 1.150608970 1.615738817 3 4.050635e+01 1.931682793 3 1.285673e+00 > 0.2045667699 0.1489203548 7.711538 > > "135" "E03a" 1176 128 2088 1264 0 0 3 1 1130.66667 1264.0000 980.786079 NA 6.521955 > 7.142037 1.47440896 NA 0.235464294 2 NA 0.728436654 2 NA 0.8357625114 0.5420918997 1.117925 > > "136" "E04a" 516 104 1528 1468 0 0 3 1 716.00000 1468.0000 732.764628 NA 6.074071 > 7.291656 1.35189679 NA 1.777517852 2 NA 1.559970479 2 NA 0.2174587699 0.2591289297 2.050279 > > "137" "E05a" 168 0 432 132 0 356 2 2 300.00000 244.0000 186.676190 > 158.391919 5.596195 5.378866 0.66783521 0.701541008 -0.323488724 2 1.389031e+00 -0.317317028 2 > 1.103488e+00 0.7770180413 0.7810664174 -1.229508 > > "138" "E02a" 464 0 380 268 0 0 2 1 422.00000 268.0000 59.396970 NA > 6.040028 5.590987 0.14121863 NA -3.666666643 1 NA -4.496856203 1 NA 0.1695013200 > 0.1393032210 -1.574627 > > "139" "E07a" 96 0 580 836 0 0 2 1 338.00000 836.0000 342.239682 NA > 5.463688 6.728629 1.27185876 NA 2.057851240 1 NA 1.406521521 1 NA 0.2879682878 0.3934647906 > 2.473373 > > "140" "E08a" 460 176 824 24 160 0 3 2 486.66667 92.0000 324.822003 > 96.166522 6.005294 4.126614 0.77951032 1.341466406 -1.595538586 3 1.140888e+01 -2.052931524 3 > 2.961528e+00 0.2088620248 0.1323907921 -5.289855 > > "141" "E10d" 0 0 120 68 0 0 1 1 120.00000 68.0000 NA NA 4.787492 > 4.219508 NA NA NA NA NA NA NA NA NA NA -1.764706 > > "142" "E09a" 8 0 172 200 0 0 2 1 90.00000 200.0000 115.965512 NA > 3.613468 5.298317 2.16944104 NA 1.341463416 1 NA 1.098318075 1 NA 0.4078095000 0.4701925623 > 2.222222 > > "143" "E10a" 208 0 44 216 0 0 2 1 126.00000 216.0000 115.965512 NA > 4.560864 5.375278 1.09838322 NA 1.097560977 1 NA 1.048591515 1 NA 0.4704111023 0.4849025444 > 1.714286 > > "144" "E01c" 124 0 392 412 0 0 2 1 258.00000 412.0000 189.504617 NA > 5.395772 6.021023 0.81386596 NA 1.149253734 1 NA 1.086466922 1 NA 0.4558611556 0.4736324257 > 1.596899 > > "145" "A02a" 272 0 588 612 1644 2676 2 3 430.00000 1644.0000 223.445743 1032.000000 > 5.991265 7.237899 0.54512621 0.751714932 1.560069984 3 2.133120e+01 1.979842155 3 1.901570e+00 > 0.2166496378 0.1420792749 3.823256 > > "146" "A10n" 596 128 2984 896 516 172 3 3 1236.00000 528.0000 1531.791108 362.149141 > 6.414430 6.063847 1.57463421 0.840182631 -0.779083306 4 1.789057e+01 -0.340228643 4 3.512465e+00 > 0.4794492261 0.7508008055 -2.340909 > > "147" "A01m" 440 112 428 908 0 288 3 2 326.66667 598.0000 186.003584 > 438.406204 5.621466 6.237102 0.78211434 0.811959331 1.006945660 3 5.555341e+00 0.851307744 3 > 1.077775e+00 0.3881401740 0.4571561542 1.830612 > > "148" "A14a" 0 0 80 0 1296 2136 1 2 80.00000 1716.0000 NA 593.969696 4.382027 > 7.416864 NA 0.353307546 3.895238097 1 NA 12.147795012 1 NA 0.1599805033 0.0522883020 21.450000 > > "149" "C11a" 108 0 0 840 1500 2436 1 3 108.00000 1592.0000 NA 801.967580 4.682131 > 7.281578 NA 0.533060179 3.205071455 2 NA 8.446277649 2 NA 0.0851044902 0.0137294462 14.740741 > > "150" "C12b" 1356 0 3588 3804 2152 2528 2 3 2472.00000 2828.0000 1578.262336 865.896068 > 7.698822 7.917715 0.68805432 0.293658657 0.338134551 3 3.322208e+00 0.516777969 3 5.489842e+00 > 0.7575419629 0.6409934591 1.144013 > > "151" "C06b" 800 112 1216 1172 2004 1952 3 3 709.33333 1709.3333 557.556574 466.070095 > 6.168811 7.415326 1.27333550 0.302406395 2.383451771 4 1.431118e+00 1.649683517 4 1.772980e+01 > 0.0757045623 0.1743526276 2.409774 > > "152" "C09b" 240 0 1032 948 1804 2376 2 3 636.00000 1709.3333 560.028571 718.691403 > 6.209946 7.375097 1.03139657 0.471531771 1.754913839 3 1.646890e+00 1.799973401 3 4.784422e+00 > 0.1775434070 0.1696844484 2.687631 > > "153" "C14b" 612 64 840 12 2316 2020 3 3 505.33333 1449.3333 398.844999 1253.534736 > 5.769672 5.947785 1.40394146 2.999720287 1.242956724 4 9.877896e+00 0.093146241 4 4.565239e+00 > 0.2817652114 0.9302663066 2.868074 > > "154" "C11b" 552 0 932 1556 2304 2404 2 3 742.00000 2088.0000 268.700577 463.430685 > 6.575440 7.625722 0.37037176 0.239834044 3.605443372 3 2.974626e+00 3.967992796 3 2.384812e+00 > 0.0366211721 0.0286030347 2.814016 > > "155" "C06e" 524 352 548 1564 1220 1712 3 3 474.66667 1498.6667 106.908060 252.422926 > 6.143799 7.302342 0.24366383 0.175436897 6.470021676 4 5.574895e+00 6.683277859 4 1.929036e+00 > 0.0029399907 0.0026061603 3.157303 > > "156" "B09n" 56 0 280 332 332 340 2 3 168.00000 334.6667 158.391919 > 4.618802 4.830071 5.813072 1.13804446 0.013747084 1.994794132 3 1.176000e+03 1.638636483 3 > 6.853261e+03 0.1400309567 0.1998172900 1.992063 > > "157" "C02b" 28 0 184 388 1376 1944 2 3 106.00000 1236.0000 110.308658 787.390627 > 4.273570 6.920148 1.33129203 0.848422229 1.916037228 3 5.095201e+01 2.801880431 3 2.462196e+00 > 0.1512253995 0.0677471289 11.660377 > > "158" "E13e" 1296 0 504 292 240 0 2 2 900.00000 266.0000 560.028571 > 36.769553 6.694807 5.578696 0.66783521 0.138674161 -1.597570412 2 2.319763e+02 -2.314123224 2 > 2.319250e+01 0.2512310064 0.1467226203 -3.383459 > > "159" "B06n" 52 0 528 140 652 492 2 3 290.00000 428.0000 336.582828 > 261.931289 5.110170 5.873389 1.63896927 0.819104993 0.523146114 3 1.651236e+00 0.721524435 3 > 4.003709e+00 0.6370542121 0.5227365272 1.475862 > > "160" "C12a" 36 0 2144 1440 1952 2320 2 3 1090.00000 1904.0000 1490.581095 441.959274 > 5.626974 7.532777 2.88988148 0.241464562 0.955539189 3 1.137488e+01 1.242619558 3 1.432364e+02 > 0.4097982329 0.3022846530 1.746789 > > "161" "A10m" 1888 1952 4828 3136 2084 1764 3 3 2889.33333 2328.0000 1679.239510 717.807774 > 7.867357 7.722696 0.53271982 0.296039601 -0.532387023 4 5.472792e+00 -0.411124812 4 3.238158e+00 > 0.6226570518 0.7020532942 -1.241123 > > "162" "A11m" 892 1552 2988 2356 528 1412 3 3 1810.66667 1432.0000 1071.674080 914.164099 > 7.381042 7.095526 0.60515264 0.760108777 -0.465615070 4 1.374286e+00 -0.508991835 4 1.577690e+00 > 0.6657128830 0.6375498929 -1.264432 > > "163" "A11l" 124 200 836 900 336 636 3 3 386.66667 624.0000 390.985081 > 282.191424 5.615743 6.358235 0.99298346 0.499747355 0.852524044 4 1.919697e+00 1.156870407 4 > 3.948053e+00 0.4419610495 0.3117081595 1.613793 > > "164" "A12l" 92 80 1096 664 772 748 3 3 422.66667 728.0000 583.154639 > 56.709788 5.301079 6.588223 1.47246755 0.079475763 0.902624708 4 1.057429e+02 1.511855717 4 > 3.432591e+02 0.4177655924 0.2051069822 1.722397 > > "165" "A12m" 688 552 2488 1148 680 1260 3 3 1242.66667 1029.3333 1080.631914 307.670820 > 6.888857 6.902245 0.81322076 0.332495850 -0.328864005 4 1.233624e+01 0.026393745 4 5.981973e+00 > 0.7587560326 0.9802075636 -1.207254 > > "166" "A06k" 36 448 932 780 0 532 3 2 472.00000 656.0000 448.481884 > 175.362482 5.508548 6.467969 1.70688523 0.270574714 0.530533839 3 6.540583e+00 0.749427909 3 > 3.979552e+01 0.6325043242 0.5080128786 1.389831 > > "167" "A12j" 652 208 708 960 948 1160 3 3 522.66667 1022.6667 273.944033 > 119.085404 6.126676 6.925821 0.68465386 0.113065164 2.899234362 4 5.291839e+00 1.994676390 4 > 3.666777e+01 0.0441518340 0.1168246949 1.956633 > > "168" "A05n" 3032 1776 3468 2548 2700 1888 3 3 2758.66667 2378.6667 878.492648 431.672716 > 7.883477 7.762448 0.35401820 0.192009221 -0.672420407 4 4.141590e+00 -0.520510424 4 3.399437e+00 > 0.5381608754 0.6301908844 -1.159753 > > "169" "A07n" 260 0 72 592 0 200 2 2 166.00000 396.0000 132.936075 > > > > > _______________________________________________ > Genex-dev mailing list > Gen...@li... > http://lists.sourceforge.net/lists/listinfo/genex-dev |
