Hi January, Thanks for the answer and help. I have already tried this package, but unfortunately it gives me an error due to some singularity related issues in the LAPACK routine. I have not seen people using the biclustering package, but I don't know if it will give me what I want (basically the clustering pattern in the heatmap). Thanks, S. On Thu, Sep 16, 2010 at 7:46 AM, January Weiner < january.weiner@mpiib-berlin.mpg.de> wrote: > Dear Sunny, > > I think a better approach would be to use a package like pvclust. > Pvclust creates a hierarchical clustering (a tree), and at each node > computes a p-value; therefore, the criterion to choose certain > clusters can be defined by a threshold p value. > > See http://www.is.titech.ac.jp/~shimo/prog/pvclust/ for details. > > Best regards, > > January > > On Thu, Sep 16, 2010 at 12:57 PM, Sunny Srivastava > <research.baba@gmail.com> wrote: > > Hello Bioconductor Helpers, > > I have a question about extracting the clusters of genes after we make > the > > heatmap (say ht4) using the heatmap.2 function. Basically, I want to get > the > > clusters which are shown as row dendrogram in the heatmap. > > > > I understand that ht4$rowDendrogram is an object of dendrogram and it > > containes details of all the nodes and branches, but lets say I want to > know > > the number of clusters and the genes in each cluster if I terminated the > > tree (dendrogram) at a particular height. Also, if I know that I want 12 > > clusters, how do I know which height I should terminate the tree (or > > branching structure) > > > > I am sorry I am not clear. Please let me know if you need any further > > clarifications. Thanks in advance for your help. > > > > Best Regards, > > S. > > > > > > Below is the dump of the matrix *row.scaled.fc2* and the object *ht4* > which > > was obtained by using the heatmap.2 function. > > > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- ------- > > Dump of the matrix row.scaled.fc2 of dimension 47X4 for which I need to > get > > the cluster > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- ------- > > row.scaled.fc2 <- > > structure(c(1.28370586906697, 0.045882176168387, -1.36708804887146, > > 0.521861081643557, 0.931917365795697, -1.26811754842825, > > -0.72130612803134, > > 0.997233560332114, 1.10914280037357, 0.906822512746599, > > 0.124305385892705, > > 0.243716750638903, -0.81506628597585, 0.9281945227055, > > -1.02514155647985, > > -0.0148828263869010, 0.610771143828774, -1.31512789127346, > > -1.03419747081316, > > -1.37364737258546, 1.25426184614502, -0.901983912371582, > > 1.39208493297302, > > 1.46330419386939, 1.46904838309704, 1.33893188130515, > > 1.19407808189758, > > 1.2218547353343, 1.19698274357976, 1.18155526998177, > > 0.841732283108634, > > 0.747807260442244, 0.714318042078153, -1.33532716080095, > > -0.313607205847584, > > 0.355541486307312, -0.116351310506438, 0.77912190137299, > > 1.19372966187956, > > -1.46614749631243, 1.05871763558761, -0.943184299406566, > > 1.03714731356991, > > 1.25047276064487, 0.851530489918317, 0.97326112450597, > > 0.776853817614179, > > 0.254354524536168, 1.31978778177031, 1.03174081073449, > > 1.03284070831524, > > 0.653353551741362, -0.215733545477378, -0.966047927590969, > > 0.652368565446036, > > 0.536560120952493, 0.807139899513123, 1.26763097889282, > > 1.28335333872251, > > 1.45704025225707, 0.57691754078049, 1.07113369815538, > > 0.610158458070122, > > -0.762088920575592, 1.00819322156949, 1.14148232415467, > > 0.297815716619546, > > 0.143195107796418, -0.0065855621849476, 0.062650188298147, > > -0.177601977084224, > > -0.437288024655434, 0.178377570495840, 0.447251122498145, > > 0.400521563178456, > > 0.441487949431983, 0.465093691295555, 0.754248218272813, > > 0.657576754588525, > > 0.832332574891687, -0.194585070239614, 1.09572866565514, > > 1.04256940502540, > > 0.583290457043162, 0.947182223637108, 0.453501818870319, > > 0.362539212141846, > > 0.64658837487362, 0.778492522245523, 0.406650195058153, > > -0.113538768459753, > > 0.596257630693658, 0.652082611403661, 0.731202922578465, > > -0.540351240198989, > > -0.280636135117373, 0.0957282195118376, > -0.301771114678491, > > -0.319287162711085, > > 0.392333008215492, 0.595799016736027, -0.493631246722725, > > -0.570129842719142, > > -0.687622802632555, -0.243797611378268, > -0.510913960310597, > > -0.263387651214153, > > -0.172495725682589, 0.609736001727743, 0.809229072877685, > > 1.08430415610192, > > 0.475088705288397, 0.503896215545131, 0.0658502505817462, > > -0.235112572720005, > > 1.39599392995549, -0.73223360450103, -0.661334598551208, > > -0.759202304177765, > > -0.86894723087327, -0.9372047007794, -0.93488345268835, > > -0.941766151100918, > > -0.949595224394993, -1.27181485347646, -1.41712359913304, > > -1.32146222297309, > > 0.698917086441383, 0.444155476463272, -0.0629413619565949, > > 0.892855986235108, > > -0.809524028729025, -0.903176468889435, 0.786326226622549, > > -0.793466237636563, > > 0.945708813261833, -0.123281411659495, 0.0548777607029143, > > -0.0638457887809093, > > -1.20425833446000, -1.35599301451107, -0.997709153404147, > > -1.08503382282132, > > 0.239619018625132, -1.25293067528031, -1.26598375482597, > > 1.09151808569014, > > 1.09155503888627, -1.15597087905543, -1.07557307860692, > > -1.02633960962716, > > -1.14813875340725, -1.01615612905082, -0.378586315067078, > > -1.33261633780340, > > -0.655728143403281, -1.40450470456092, -0.932986379355095, > > -0.168154035584431, > > -0.611181068886636, 1.00998140538417, -1.16234438122143, > > -0.487424455398969, > > -0.722501516770135, -0.624367618233957, > -0.272558054263839, > > -0.648362220927723, > > -0.704124503616327, -0.687492845824406, > -0.696704541910826, > > -0.697053736882326, > > -0.324165647904986, 0.0117395841022768, > -0.225188393996755, > > 0.830995144599174, > > -1.22627693627083, -1.33516952937611, -1.35979513277183, > > -0.91678009628107, > > -0.744055011860442, 0.317282057548041, -0.911839772824668, > > -0.78101703610078, > > -1.32051609696858, -1.19181175288804, -1.38394233183106, > > -0.421085401449625, > > -0.152063725681571), .Dim = c(47L, 4L), .Dimnames = > > list(c("pSysX_130", > > "pSysX_48", > > "pSysX_49", "pSysX_50", "sll0108", "sll0327", "sll0685", > > "sll0735", > > "sll0781", "sll0783", "sll0788", "sll0789", "sll0790", > > "sll1130", > > "sll1450", "sll1507", "sll1621", "sll1694", "sll1695", > > "sll1796", > > "sll1814", "sll1891", "slr0041", "slr0042", "slr0043", > > "slr0044", > > "slr0144", "slr0145", "slr0146", "slr0147", "slr0737", > > "slr0749", > > "slr0750", "slr0853", "slr0898", "slr1236", "slr1251", > > "slr1603", > > "slr1634", "slr1675", "slr1930", "slr1984", "smr0003", > > "ssl2148", > > "ssl2245", "ssr0390", "ssr1251"), c("l1", "d1", "l13", > > > > "d13"))) > > > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------- > > > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------- > > Dump of the object ht4 obtained by using heatmap.2 on a given data set > > (matrix) of dimension 47 x 4 > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- --------- > > ht4 <- > > structure(list(rowInd = c(7L, 34L, 6L, 20L, 13L, 18L, 3L, 40L, > > 15L, 19L, 42L, 44L, 1L, 21L, 43L, 45L, 14L, 5L, 39L, > 29L, > > 27L, > > 30L, 28L, 8L, 9L, 41L, 10L, 38L, 26L, 23L, 24L, 25L, > 32L, > > 33L, > > 47L, 31L, 46L, 22L, 17L, 16L, 37L, 35L, 12L, 2L, 11L, > 4L, > > 36L > > ), colInd = 1:4, call = quote(heatmap.2(x = > > row.scaled.fc2, Colv = FALSE, > > dendrogram = "row", scale = "none", > > breaks = breaks.fc2, > > col = blue.red.fc2, trace = "none", > > cexRow = 0.8, cexCol = 2, > > labCol = colnames(row.scaled.fc2), key > = > > FALSE, density.info = "none", > > main = expression("Heatmap of " * > log[2] > > * "Int. of Genes (with Adjusted P Value <0.01 & FC>1.5or<0.7) for > > Treatments"), > > xlab = "Treatments", ylab = "Genes in > > the Microarray Adjusted P Value less than 0.01 and Fold Change above 1.5 > or > > below 0.7", > > lmat = rbind(c(0, 3), c(2, 1), c(0, > 4)), > > lhei = c(0.25, 4, > > > > 0.25), cex = 1.5)), carpet = structure(c(-0.72130612803134, > > > > -0.966047927590969, 0.595799016736027, > 1.09155503888627, > > -1.33532716080095, > > > > -0.194585070239614, 0.698917086441383, > > 0.830995144599174, -1.26811754842825, > > > > -0.215733545477378, 0.392333008215492, > 1.09151808569014, > > -1.37364737258546, > > > > 0.297815716619546, 0.0658502505817462, > 1.00998140538417, > > -0.81506628597585, > > > > 1.45704025225707, -0.263387651214153, > > -0.378586315067078, -1.31512789127346, > > > > 1.00819322156949, 0.475088705288397, > -0.168154035584431, > > -1.36708804887146, > > > > 1.03174081073449, 0.0957282195118376, > 0.239619018625132, > > -1.46614749631243, > > > > 0.362539212141846, 0.786326226622549, > 0.317282057548041, > > -1.02514155647985, > > > > 1.07113369815538, 0.609736001727743, > -0.655728143403281, > > -1.03419747081316, > > > > 1.14148232415467, 0.503896215545131, > -0.611181068886636, > > -0.943184299406566, > > > > 0.778492522245523, 0.945708813261833, > -0.78101703610078, > > 1.25047276064487, > > > > -0.113538768459753, 0.0548777607029143, > > -1.19181175288804, 1.28370586906697, > > > > 0.254354524536168, -0.540351240198989, > > -0.997709153404147, 1.25426184614502, > > > > 0.143195107796418, -0.235112572720005, > > -1.16234438122143, 1.03714731356991, > > > > 0.406650195058153, -0.123281411659495, > > -1.32051609696858, 0.851530489918317, > > > > 0.596257630693658, -0.0638457887809093, > > -1.38394233183106, 0.9281945227055, > > > > 0.57691754078049, -0.172495725682589, > -1.33261633780340, > > 0.931917365795697, > > > > 0.653353551741362, -0.319287162711085, > > -1.26598375482597, 1.19372966187956, > > > > 0.453501818870319, -0.903176468889435, > > -0.744055011860442, 1.19698274357976, > > > > 0.441487949431983, -0.941766151100918, > > -0.696704541910826, 1.19407808189758, > > > > 0.447251122498145, -0.9372047007794, > -0.704124503616327, > > 1.18155526998177, > > > > 0.465093691295555, -0.949595224394993, > > -0.697053736882326, 1.2218547353343, > > > > 0.400521563178456, -0.93488345268835, > > -0.687492845824406, 0.997233560332114, > > > > 0.652368565446036, -0.493631246722725, > > -1.15597087905543, 1.10914280037357, > > > > 0.536560120952493, -0.570129842719142, > > -1.07557307860692, 1.05871763558761, > > > > 0.64658837487362, -0.793466237636563, > > -0.911839772824668, 0.906822512746599, > > > > 0.807139899513123, -0.687622802632555, > > -1.02633960962716, 0.77912190137299, > > > > 0.947182223637108, -0.809524028729025, > > -0.91678009628107, 1.33893188130515, > > > > 0.178377570495840, -0.86894723087327, > > -0.648362220927723, 1.39208493297302, > > > > 0.062650188298147, -0.73223360450103, > > -0.722501516770135, 1.46330419386939, > > > > -0.177601977084224, -0.661334598551208, > > -0.624367618233957, 1.46904838309704, > > > > -0.437288024655434, -0.759202304177765, > > -0.272558054263839, 0.747807260442244, > > > > 0.657576754588525, -1.41712359913304, > > 0.0117395841022768, 0.714318042078153, > > > > 0.832332574891687, -1.32146222297309, > > -0.225188393996755, 0.776853817614179, > > > > 0.731202922578465, -1.35599301451107, > > -0.152063725681571, 0.841732283108634, > > > > 0.754248218272813, -1.27181485347646, > > -0.324165647904986, 0.97326112450597, > > > > 0.652082611403661, -1.20425833446000, > > -0.421085401449625, -0.901983912371582, > > > > -0.0065855621849476, 1.39599392995549, > > -0.487424455398969, 0.610771143828774, > > > > -0.762088920575592, 1.08430415610192, > > -0.932986379355095, -0.0148828263869010, > > > > 0.610158458070122, 0.809229072877685, > -1.40450470456092, > > -0.116351310506438, > > > > 0.583290457043162, 0.892855986235108, > -1.35979513277183, > > -0.313607205847584, > > > > 1.09572866565514, 0.444155476463272, > -1.22627693627083, > > 0.243716750638903, > > > > 1.28335333872251, -0.510913960310597, > -1.01615612905082, > > 0.045882176168387, > > > > 1.31978778177031, -0.280636135117373, > -1.08503382282132, > > 0.124305385892705, > > > > 1.26763097889282, -0.243797611378268, > -1.14813875340725, > > 0.521861081643557, > > > > 1.03284070831524, -0.301771114678491, > -1.25293067528031, > > 0.355541486307312, > > > > 1.04256940502540, -0.0629413619565949, > > -1.33516952937611), .Dim = c(4L, > > > > > > 47L), .Dimnames = list(c("l1", "d1", "l13", "d13"), c("sll0685", > > > > > > "slr0853", "sll0327", "sll1796", "sll0790", "sll1694", > "pSysX_49", > > > > > > "slr1675", "sll1450", "sll1695", "slr1984", "ssl2148", > > "pSysX_130", > > > > > > "sll1814", "smr0003", "ssl2245", "sll1130", "sll0108", "slr1634", > > > > > > "slr0146", "slr0144", "slr0147", "slr0145", "sll0735", "sll0781", > > > > > > "slr1930", "sll0783", "slr1603", "slr0044", "slr0041", "slr0042", > > > > > > "slr0043", "slr0749", "slr0750", "ssr1251", "slr0737", "ssr0390", > > > > > > "sll1891", "sll1621", "sll1507", "slr1251", "slr0898", "sll0789", > > > > > > "pSysX_48", "sll0788", "pSysX_50", "slr1236"))), rowDendrogram = > > structure(list( > > > > > > > > structure(list(structure(list(structure(7L, members = 1L, height = 0, > label > > = "sll0685", leaf = TRUE, value = structure(-2.3037127760972e-15, .Names > = > > "sll0685")), > > > > > > > > structure(list(structure(list(structure(34L, label = > "slr0853", > > members = 1L, height = 0, leaf = TRUE, value = > > structure(-2.11636264069170e-15, .Names = "slr0853")), > > > > > > > > structure(6L, label = "sll0327", > > members = 1L, height = 0, leaf = TRUE, value = > > structure(-1.38777878078145e-17, .Names = "sll0327"))), members = 2L, > > midpoint = 0.5, height = 0.408448760380633, value = > -2.13024042849952e-15), > > > > > > > > structure(20L, members = 1L, height = 0, label > = > > "sll1796", leaf = TRUE, value = structure(1.05818132034585e-15, .Names = > > "sll1796"))), members = 3L, midpoint = 1.25, height = 0.822640063299773, > > value = -1.07205910815367e-15)), members = 4L, midpoint = 1.125, height = > > 1.5200001193864, value = -3.37577188425087e-15), > > > > > > > > structure(list(structure(13L, members = 1L, height = 0, label = > "sll0790", > > leaf = TRUE, value = structure(-2.12330153459561e-15, .Names = > "sll0790")), > > > > > > > > structure(list(structure(list(structure(list(structure(18L, > > label = "sll1694", members = 1L, height = 0, leaf = TRUE, value = > > structure(-1.06165076729781e-15, .Names = "sll1694")), > > > > > > > > structure(3L, > label > > = "pSysX_49", members = 1L, height = 0, leaf = TRUE, value = > > structure(3.12250225675825e-17, .Names = "pSysX_49"))), members = 2L, > > midpoint = 0.5, height = 0.55986390207006, value = > -1.03042574473022e-15), > > > > > > > > structure(40L, members = 1L, > > height = 0, label = "slr1675", leaf = TRUE, value = > > structure(2.59514632006130e-15, .Names = "slr1675"))), members = 3L, > > midpoint = 1.25, height = 0.96984571387736, value = > 1.56472057533108e-15), > > > > > > > > structure(list(structure(list(structure(15L, > > label = "sll1450", members = 1L, height = 0, leaf = TRUE, value = > > structure(-7.4940054162198e-16, .Names = "sll1450")), > > > > > > > > structure(19L, > > label = "sll1695", members = 1L, height = 0, leaf = TRUE, value = > > structure(1.72084568816899e-15, .Names = "sll1695"))), members = 2L, > > midpoint = 0.5, height = 0.134972000620768, value = > 9.71445146547012e-16), > > > > > > > > structure(42L, members = 1L, > > height = 0, label = "slr1984", leaf = TRUE, value = > > structure(2.35922392732846e-15, .Names = "slr1984"))), members = 3L, > > midpoint = 1.25, height = 0.603396735921129, value = > 3.33066907387547e-15)), > > members = 6L, midpoint = 2.75, height = 1.41703706740193, value = > > 4.89538964920655e-15)), members = 7L, midpoint = 1.875, height = > > 1.79108103853389, value = 2.77208811461094e-15)), members = 11L, midpoint > = > > 3.5, height = 2.96304988576369, value = -6.03683769639929e-16), > > > > > > > > structure(list(structure(list(structure(list(structure(list( > > > > > > > > structure(list(structure(44L, > > members = 1L, height = 0, label = "ssl2148", leaf = TRUE, value = > > structure(-2.68535194081210e-15, .Names = "ssl2148")), > > > > > > > > > > structure(list(structure(1L, label = "pSysX_130", members = 1L, height = > 0, > > leaf = TRUE, value = structure(-3.88578058618805e-16, .Names = > > "pSysX_130")), > > > > > > > > > > structure(21L, label = "sll1814", members = 1L, height = 0, leaf = TRUE, > > value = structure(2.77555756156289e-17, .Names = "sll1814"))), members = > 2L, > > midpoint = 0.5, height = 0.36537483325832, value = > -3.60822483003176e-16)), > > members = 3L, midpoint = 0.75, height = 0.72692729840601, value = > > -3.04617442381527e-15), > > > > > > > > > > structure(list(structure(list(structure(43L, members = 1L, height = 0, > label > > = "smr0003", leaf = TRUE, value = structure(-3.63598040564739e-15, .Names > = > > "smr0003")), > > > > > > > > > > structure(list(structure(45L, label = "ssl2245", members = 1L, height = > 0, > > leaf = TRUE, value = structure(8.22258927613007e-16, .Names = > "ssl2245")), > > > > > > > > > > structure(14L, label = "sll1130", members = 1L, height = 0, > leaf > > = TRUE, value = structure(1.38083988687754e-15, .Names = "sll1130"))), > > members = 2L, midpoint = 0.5, height = 0.143842203308732, value = > > 2.20309881449055e-15)), members = 3L, midpoint = 0.75, height = > > 0.279213297331223, value = -1.43288159115684e-15), > > > > > > > > structure(5L, > > members = 1L, height = 0, label = "sll0108", leaf = TRUE, value = > > structure(1.19348975147204e-15, .Names = "sll0108"))), members = 4L, > > midpoint = 1.875, height = 0.336642122872617, value = > > -2.39391839684799e-16)), members = 7L, midpoint = 2.8125, height = > > 0.913839289019599, value = -3.28556626350007e-15), > > > > > > > > > > structure(list(structure(list(structure(list(structure(39L, members = > 1L, > > height = 0, label = "slr1634", leaf = TRUE, value = > > structure(-3.46944695195361e-16, .Names = "slr1634")), > > > > > > > > > > structure(list(structure(list(structure(29L, label = "slr0146", members = > > 1L, height = 0, leaf = TRUE, value = structure(-2.22044604925031e-16, > .Names > > = "slr0146")), > > > > > > > > > > structure(27L, label = "slr0144", members = 1L, > > height = 0, leaf = TRUE, value = structure(1.94289029309402e-16, .Names = > > "slr0144"))), members = 2L, midpoint = 0.5, height = 0.0108403820977512, > > value = -2.77555756156289e-17), > > > > > > > > > > structure(30L, members = 1L, height = 0, label = "slr0147", > leaf > > = TRUE, value = structure(2.35922392732846e-16, .Names = "slr0147"))), > > members = 3L, midpoint = 1.25, height = 0.0292686575762982, value = > > 2.08166817117217e-16)), members = 4L, midpoint = 1.125, height = > > 0.068164565843679, value = -1.38777878078145e-16), > > > > > > > > structure(28L, > > members = 1L, height = 0, label = "slr0145", leaf = TRUE, value = > > structure(0, .Names = "slr0145"))), members = 5L, midpoint = 2.5625, > height > > = 0.088331980043033, value = -1.38777878078145e-16), > > > > > > > > > > structure(list(structure(list(structure(list(structure(8L, label = > > "sll0735", members = 1L, height = 0, leaf = TRUE, value = > > structure(-1.65145674912992e-15, .Names = "sll0735")), > > > > > > > > > > structure(9L, label = "sll0781", members = 1L, height = 0, leaf > = > > TRUE, value = structure(4.9960036108132e-16, .Names = "sll0781"))), > members > > = 2L, midpoint = 0.5, height = 0.195578923529741, value = > > -1.1518563880486e-15), > > > > > > > > > > structure(41L, members = 1L, height = 0, label = "slr1930", leaf = TRUE, > > value = structure(7.7715611723761e-16, .Names = "slr1930"))), members = > 3L, > > midpoint = 1.25, height = 0.39155423751868, value = > -3.7470027081099e-16), > > > > > > > > > > structure(list(structure(10L, label = "sll0783", members = 1L, height = > 0, > > leaf = TRUE, value = structure(4.16333634234434e-16, .Names = > "sll0783")), > > > > > > > > > > structure(38L, label = "slr1603", members = 1L, height = 0, leaf = TRUE, > > value = structure(6.10622663543836e-16, .Names = "slr1603"))), members = > 2L, > > midpoint = 0.5, height = 0.250564352172644, value = > 1.02695629777827e-15)), > > members = 5L, midpoint = 2.375, height = 0.600040909040007, value = > > 6.5225602696728e-16)), members = 10L, midpoint = 4.96875, height = > > 0.750425125084372, value = 5.13478148889135e-16)), members = 17L, > midpoint = > > 7.390625, height = 1.47313730565769, value = -2.77208811461094e-15), > > > > > > > > structure(list(structure(list(structure(list(structure(list( > > > > > > > > > > structure(26L, label = "slr0044", members = 1L, height = 0, leaf = TRUE, > > value = structure(-6.59194920871187e-16, .Names = "slr0044")), > > > > > > > > > > structure(23L, label = "slr0041", members = 1L, height = 0, leaf = TRUE, > > value = structure(2.42861286636753e-17, .Names = "slr0041"))), members = > 2L, > > midpoint = 0.5, height = 0.201010757711608, value = > -6.34908792207511e-16), > > > > > > > > structure(24L, > > members = 1L, height = 0, label = "slr0042", leaf = TRUE, value = > > structure(0, .Names = "slr0042"))), members = 3L, midpoint = 1.25, height > = > > 0.431124873425334, value = -6.34908792207511e-16), > > > > > > > > structure(25L, members = 1L, > > height = 0, label = "slr0043", leaf = TRUE, value = > > structure(6.66133814775094e-16, .Names = "slr0043"))), members = 4L, > > midpoint = 2.125, height = 0.741112103334488, value = > > 3.12250225675825e-17), > > > > > > > > structure(list(structure(32L, members = 1L, > > height = 0, label = "slr0749", leaf = TRUE, value = > > structure(2.59774840527527e-16, .Names = "slr0749")), > > > > > > > > > > structure(list(structure(list(structure(list( > > > > > > > > > > structure(33L, label = "slr0750", members = 1L, height = 0, > leaf > > = TRUE, value = structure(-2.84494650060196e-16, .Names = "slr0750")), > > > > > > > > > > structure(47L, label = "ssr1251", members = 1L, height = 0, > leaf > > = TRUE, value = structure(2.08166817117217e-17, .Names = "ssr1251"))), > > members = 2L, midpoint = 0.5, height = 0.143796809698028, value = > > -2.63677968348475e-16), > > > > > > > > > > structure(31L, members = 1L, height = 0, label = "slr0737", leaf = TRUE, > > value = structure(-4.16333634234434e-17, .Names = "slr0737"))), members = > > 3L, midpoint = 1.25, height = 0.203581274597441, value = > > -3.05311331771918e-16), > > > > > > > > structure(46L, > > members = 1L, height = 0, label = "ssr0390", leaf = TRUE, value = > > structure(1.81799020282369e-15, .Names = "ssr0390"))), members = 4L, > > midpoint = 2.125, height = 0.38942773178888, value = > 1.51267887105178e-15)), > > members = 5L, midpoint = 1.5625, height = 0.532455368507944, value = > > 1.77245371157930e-15)), members = 9L, midpoint = 3.84375, height = > > 1.58111810294058, value = 1.80367873414689e-15)), members = 26L, midpoint > = > > 14.1171875, height = 2.11249037373193, value = -9.68409380464053e-16), > > > > > > > > structure(list(structure(list(structure(22L, label = "sll1891", members > = > > 1L, height = 0, leaf = TRUE, value = structure(-1.26287869051112e-15, > .Names > > = "sll1891")), > > > > > > > > structure(17L, label = "sll1621", members = 1L, > > height = 0, leaf = TRUE, value = structure(1.08246744900953e-15, .Names = > > "sll1621"))), members = 2L, midpoint = 0.5, height = 1.77620075661612, > value > > = -1.80411241501588e-16), > > > > > > > > structure(list(structure(list(structure(list(structure(16L, > > label = "sll1507", members = 1L, height = 0, leaf = TRUE, value = > > structure(-2.86055901188575e-15, .Names = "sll1507")), > > > > > > > > structure(37L, > > label = "slr1251", members = 1L, height = 0, leaf = TRUE, value = > > structure(1.68962066560141e-15, .Names = "slr1251"))), members = 2L, > > midpoint = 0.5, height = 0.141457234512609, value = > -1.17093834628434e-15), > > > > > > > > structure(35L, members = 1L, > > height = 0, label = "slr0898", leaf = TRUE, value = > > structure(-1.12410081243297e-15, .Names = "slr0898"))), members = 3L, > > midpoint = 1.25, height = 0.721569166579802, value = > > -2.29503915871732e-15), > > > > > > > > structure(list(structure(list(structure(12L, > > members = 1L, height = 0, label = "sll0789", leaf = TRUE, value = > > structure(-6.93889390390723e-18, .Names = "sll0789")), > > > > > > > > > > structure(list(structure(2L, label = "pSysX_48", members = 1L, height = > 0, > > leaf = TRUE, value = structure(-3.98986399474666e-17, .Names = > > "pSysX_48")), > > > > > > > > > > structure(11L, label = "sll0788", members = 1L, height = 0, leaf = TRUE, > > value = structure(5.93275428784068e-16, .Names = "sll0788"))), members = > 2L, > > midpoint = 0.5, height = 0.119205037667866, value = > 5.53376788836601e-16)), > > members = 3L, midpoint = 0.75, height = 0.321367116594267, value = > > 5.46437894932694e-16), > > > > > > > > structure(list(structure(4L, > label > > = "pSysX_50", members = 1L, height = 0, leaf = TRUE, value = > > structure(-8.04911692853238e-16, .Names = "pSysX_50")), > > > > > > > > structure(36L, > > label = "slr1236", members = 1L, height = 0, leaf = TRUE, value = > > structure(3.21270787750905e-15, .Names = "slr1236"))), members = 2L, > > midpoint = 0.5, height = 0.302588392442079, value = > 2.40779618465581e-15)), > > members = 5L, midpoint = 2.125, height = 0.610680499686294, value = > > 2.9542340795885e-15)), members = 8L, midpoint = 3.1875, height = > > 1.64572016900367, value = 6.59194920871187e-16)), members = 10L, midpoint > = > > 2.84375, height = 2.62534326555191, value = 4.78783679369599e-16)), > members > > = 36L, midpoint = 21.48046875, height = 3.36537033143646, value = > > -4.89625701094454e-16)), members = 47L, midpoint = 17.990234375, height = > > 3.46289882269828, class = "dendrogram", value = -1.09330947073438e-15), > > breaks = structure(c(-1.46614749631243, > > -1.32889829952663, > > -1.17216683844364, -0.966047927590969, > > -0.890971685205478, > > -0.721704590944272, -0.611181068886636, > > -0.317393843756585, > > -0.0065855621849476, 0, 0.247262675271325, > > 0.446219240486521, > > 0.596257630693658, 0.719946335578257, > 0.831886764794183, > > 0.997233560332114, 1.09153040342218, 1.25299881764497, > > 1.46904838309704 > > ), .Names = c("0%", "11.111%", "22.222%", "33.333%", > > "44.444%", > > "55.556%", "66.667%", "77.778%", "100%", "", > > "11.111%", "22.222%", > > "33.333%", "44.444%", "55.556%", "66.667%", > "77.778%", > > "88.889%", > > "100%")), col = c("#0000FF", "#2020FF", "#4040FF", > > "#6060FF", > > "#8080FF", "#9F9FFF", "#BFBFFF", > "#DFDFFF", > > "#FFFFFF", "#FFFFFF", > > "#FFDFDF", "#FFBFBF", "#FF9F9F", > "#FF8080", > > "#FF6060", "#FF4040", > > "#FF2020", "#FF0000"), colorTable = > > structure(list(low = c(-1.46614749631243, > > > > -1.32889829952663, -1.17216683844364, -0.966047927590969, > > > > -0.890971685205478, -0.721704590944272, -0.611181068886636, > > > > -0.317393843756585, -0.0065855621849476, 0, 0.247262675271325, > > > > 0.446219240486521, 0.596257630693658, 0.719946335578257, > > > > 0.831886764794183, 0.997233560332114, 1.09153040342218, > > 1.25299881764497 > > > > ), high = c(-1.32889829952663, -1.17216683844364, > -0.966047927590969, > > > > -0.890971685205478, -0.721704590944272, -0.611181068886636, > > > > -0.317393843756585, -0.0065855621849476, 0, 0.247262675271325, > > > > 0.446219240486521, 0.596257630693658, 0.719946335578257, > > > > 0.831886764794183, 0.997233560332114, 1.09153040342218, > > 1.25299881764497, > > > > 1.46904838309704), color = structure(c(1L, 2L, 3L, 4L, 5L, > > > > 6L, 7L, 8L, 17L, 17L, 16L, 15L, 14L, 13L, 12L, > > 11L, 10L, > > > > 9L), .Label = c("#0000FF", "#2020FF", > "#4040FF", > > "#6060FF", > > > > "#8080FF", "#9F9FFF", "#BFBFFF", > "#DFDFFF", > > "#FF0000", "#FF2020", > > > > "#FF4040", "#FF6060", "#FF8080", > "#FF9F9F", > > "#FFBFBF", "#FFDFDF", > > > > "#FFFFFF"), class = "factor")), .Names = > > c("low", "high", > > > > "color"), > > row.names = c(NA, -18L), class = "data.frame")), .Names = c("rowInd", > > > > > > "colInd", "call", > "carpet", > > "rowDendrogram", "breaks", "col", > > > > > > "colorTable")) > > > > > -------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ------------------- > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > -------- Dr. January Weiner 3 -------------------------------------- > Max Planck Institute for Infection Biology > Charitéplatz 1 > D-10117 Berlin, Germany > Web : www.mpiib-berlin.mpg.de > Tel : +49-30-28460514 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Dear Dr. Huber, Thanks for your reply, but I had looked at this function. What I understood from the documentation was: if give the height at which I want to cut, then it gives me $upper and $lower, but I guess I have to "hack" to get the height which gives me a specific number of clusters? I am I thinking correctly? Best Regards, S. On Fri, Sep 17, 2010 at 10:11 AM, Wolfgang Huber <whuber@embl.de> wrote: > Sunny > > the function "cut.dendrogram" from the "stats" package does what you want. > It's described in the manual page of the "dendrogram" class. Try typing, in > R: > > ? dendrogram > > Best wishes > Wolfgang > > > > > On Sep/16/10 12:57 PM, Sunny Srivastava wrote: > >> Hello Bioconductor Helpers, >> I have a question about extracting the clusters of genes after we make the >> heatmap (say ht4) using the heatmap.2 function. Basically, I want to get >> the >> clusters which are shown as row dendrogram in the heatmap. >> >> I understand that ht4$rowDendrogram is an object of dendrogram and it >> containes details of all the nodes and branches, but lets say I want to >> know >> the number of clusters and the genes in each cluster if I terminated the >> tree (dendrogram) at a particular height. Also, if I know that I want 12 >> clusters, how do I know which height I should terminate the tree (or >> branching structure) >> >> I am sorry I am not clear. Please let me know if you need any further >> clarifications. Thanks in advance for your help. >> >> Best Regards, >> S. >> >> >> Below is the dump of the matrix *row.scaled.fc2* and the object *ht4* >> which >> was obtained by using the heatmap.2 function. >> >> -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]