Page Comparison

R version 2.13.0 64 bit, SageBionetworksCoex 0.11, running time \~4.5 hours (~27k by 486)

 !CorHeatmap.jpg|thumbnail!   !ScaleFree.jpg|thumbnail! !GeneDendrogram.jpg|thumbnail!

beta=6, R=0.89. Number of modules: 18 + 1 (grey):
|| Module || \# of probes || Module || \# of probes ||
| black | 108 | pink | 97 |
| blue | 1206 | purple | 89 |
| brown | 615 | red | 113 |
| cyan | 43 | salmon | 46 |
| greenyellow | 86 | tan | 85 |
| grey | 22115 | turquoise | 2151 |
| grey60 | 33 | yellow | 469 |
| lightcyan | 34 | lightgreen | 32 |
| magenta | 92 | green | 121 |
| midnightblue | 43 | | |
Analysis of the first PC of each module:

 !PercentVarianceExplainedEigen1_Eigen1variablity.png|thumbnail! !PercentVarianceExplained_Eigen1_variablity.png|thumbnail!

With M value almost no modules were composed of the CpGs from a single chromosome (chromosomal density plots can be found [here|^Histogram_chromosomal_distr.pdf])

Modules lightcyan, lightgreen, salmon and yellow, >55% of the loci came from the same chromosome (plots are [here|^GeneModuleDistrib.pdf])

Gene Ontology analyses of each module (top 10 categories were selected and KEGG pathways didn't work for my on that day):
{csv}black,CC,1.09E-10,5.64,8.61,30,1621,extracellular region,1.16E-08
black,MF,1.81E-06,11.25,0.85,8,161,sugar binding,3.11E-04
black,BP,7.73E-06,6.91,1.75,10,354,innate immune response,6.83E-03
black,BP,1.63E-05,4.62,3.82,14,772,defense response,1.44E-02
black,BP,2.40E-05,Inf,0.01,2,2,virion transport,2.12E-02
black,BP,2.40E-05,Inf,0.01,2,2,intracellular virion transport,2.12E-02
black,MF,4.32E-05,6.20,1.70,9,323,carbohydrate binding,7.43E-03
black,MF,5.97E-05,4.87,2.68,11,510,calcium ion binding,1.03E-02
black,BP,7.18E-05,417.48,0.01,2,3,peptide antigen transport,6.34E-02
black,BP,8.37E-05,4.14,3.86,13,780,immune response,7.40E-02 
blue, CC,1.86E-10,1.76,128.76,196,1855,plasma membrane part,8.71E-08
blue,CC,3.93E-09,1.56,218.36,292,3146,plasma membrane,1.85E-06
blue,CC,8.56E-09,1.54,221.76,294,3195,cell periphery,4.01E-06
blue,CC,2.36E-08,1.82,76.42,124,1101,intrinsic to plasma membrane,1.11E-05
blue,CC,6.28E-08,1.79,75.31,121,1085,integral to plasma membrane,2.95E-05
blue,BP,1.31E-07,1.98,48.18,85,707,cell adhesion,5.39E-04
blue,BP,1.31E-07,1.98,48.18,85,707,biological adhesion,5.39E-04
blue,CC,2.05E-07,1.43,390.92,463,5632,membrane,9.62E-05
blue,BP,4.90E-07,6.13,3.34,15,49,cellular defense response,2.02E-03
blue,CC,2.19E-06,3.05,10.69,28,154,anchoring junction,1.03E-03
brown,CC,4.68E-14,2.46,380.34,449,9154,intracellular,2.24E-11
brown,CC,2.12E-13,2.00,286.94,366,6906,intracellular membrane-bounded organelle,1.01E-10
brown,CC,2.78E-13,1.99,287.35,366,6916,membrane-bounded organelle,1.33E-10
brown,CC,5.90E-13,2.29,372.78,440,8972,intracellular part,2.83E-10
brown,CC,9.12E-12,1.95,316.81,388,7625,intracellular organelle,4.37E-09
brown,CC,1.37E-11,1.94,317.48,388,7641,organelle,6.56E-09
brown,CC,1.98E-10,1.77,183.61,252,4419,intracellular organelle part,9.47E-08
brown,CC,8.68E-10,1.73,186.06,252,4478,organelle part,4.16E-07
brown,CC,1.63E-09,1.94,77.28,128,1860,intracellular organelle lumen,7.78E-07
brown,CC,5.39E-09,1.88,80.40,130,1935,membrane-enclosed lumen,2.58E-06
cyan,CC,1.79E-04,3.62,7.06,17,2371,protein complex,2.34E-02
cyan,BP,3.41E-04,4.60,2.87,10,985,transcription from RNA polymerase II promoter,2.91E-01
cyan,BP,4.45E-04,80.91,0.03,2,11,protein destabilization,3.81E-01
cyan,BP,4.45E-04,80.91,0.03,2,11,"regulation of DNA damage response, signal transduction by p53 class mediator",3.81E-01
cyan,BP,4.54E-04,5.65,21.11,30,7248,metabolic process,3.88E-01
cyan,BP,5.53E-04,5.78,1.49,7,510,cellular protein localization,4.73E-01
cyan,BP,5.54E-04,8.55,0.69,5,236,nucleocytoplasmic transport,4.74E-01
cyan,BP,5.66E-04,5.75,1.49,7,512,cellular macromolecule localization,4.84E-01
cyan,BP,5.76E-04,8.48,0.69,5,238,nuclear transport,4.92E-01
cyan,BP,6.88E-04,19.72,0.17,3,60,positive regulation of cell cycle arrest,5.88E-01
green,BP,3.91E-48,628.02,0.20,24,34,keratinization,2.66E-45
green,BP,2.67E-40,155.30,0.40,25,68,keratinocyte differentiation,1.81E-37
green,BP,5.06E-38,119.11,0.48,25,81,epidermal cell differentiation,3.44E-35
green,BP,8.57E-28,39.79,1.13,25,191,epithelial cell differentiation,5.82E-25
green,BP,2.83E-27,37.71,1.18,25,200,epidermis development,1.92E-24
green,BP,8.30E-21,19.36,2.13,25,361,epithelium development,5.64E-18
green,MF,3.13E-15,80.06,0.20,10,42,olfactory receptor activity,4.57E-13
green,BP,2.40E-14,46.87,0.34,11,58,sensory perception of smell,1.63E-11
green,BP,1.09E-12,8.07,4.73,25,799,tissue development,7.41E-10
green,BP,1.67E-12,6.56,24.69,53,4175,multicellular organismal process,1.13E-09
greenyellow,CC,2.07E-13,69.55,0.20,9,38,keratin filament,2.73E-11
greenyellow,CC,8.79E-12,25.43,0.57,11,111,intermediate filament,1.16E-09
greenyellow,CC,8.87E-11,20.14,0.71,11,137,intermediate filament cytoskeleton,1.17E-08
greenyellow,MF,2.18E-06,5.93,2.72,13,518,structural molecule activity,5.10E-04
greenyellow,BP,8.41E-06,9.05,1.04,8,200,epidermis development,8.91E-03
greenyellow,BP,4.76E-05,8.34,0.97,7,186,visual perception,5.05E-02
greenyellow,BP,4.76E-05,8.34,0.97,7,186,sensory perception of light stimulus,5.05E-02
greenyellow,MF,8.89E-05,42.64,0.09,3,17,structural constituent of eye lens,2.08E-02
greenyellow,CC,1.96E-04,3.72,4.15,13,806,cytoskeletal part,2.59E-02
greenyellow,BP,3.20E-04,26.20,0.14,3,26,phototransduction,3.40E-01
grey60,BP,5.86E-04,21.35,0.17,3,86,respiratory electron transport chain,3.45E-01
grey60,CC,9.20E-04,18.08,0.19,3,105,mitochondrial membrane part,9.38E-02
lightcyan,MF,1.33E-05,87.57,0.05,3,47,"ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism",9.86E-04
lightcyan,MF,2.65E-05,68.73,0.06,3,59,"ATPase activity, coupled to transmembrane movement of ions",1.96E-03
lightcyan,BP,4.23E-05,56.87,0.07,3,57,ATP biosynthetic process,7.14E-03
lightcyan,BP,6.57E-05,48.71,0.08,3,66,purine ribonucleoside triphosphate biosynthetic process,1.11E-02
lightcyan,BP,6.87E-05,47.94,0.08,3,67,purine nucleoside triphosphate biosynthetic process,1.16E-02
lightcyan,BP,6.87E-05,47.94,0.08,3,67,ribonucleoside triphosphate biosynthetic process,1.16E-02
lightcyan,BP,7.50E-05,46.48,0.09,3,69,nucleoside triphosphate biosynthetic process,1.27E-02
lightcyan,MF,9.10E-05,44.64,0.09,3,89,"ATPase activity, coupled to transmembrane movement of substances",6.74E-03
lightcyan,MF,9.41E-05,44.12,0.09,3,90,"hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances",6.96E-03
lightcyan,MF,9.41E-05,44.12,0.09,3,90,"ATPase activity, coupled to movement of substances",6.96E-03
lightgreen,MF,7.38E-07,13.39,1.65,10,1128,receptor activity,6.64E-05
lightgreen,BP,1.56E-06,61.86,0.09,4,56,antigen processing and presentation,8.78E-04
lightgreen,MF,7.00E-06,10.17,2.10,10,1438,signal transducer activity,6.30E-04
lightgreen,MF,7.00E-06,10.17,2.10,10,1438,molecular transducer activity,6.30E-04
lightgreen,CC,1.20E-05,7.40,5.32,15,3146,plasma membrane,1.03E-03
lightgreen,BP,1.43E-05,706.81,0.01,2,4,cobalamin metabolic process,8.05E-03
lightgreen,BP,1.43E-05,706.81,0.01,2,4,cobalamin transport,8.05E-03
lightgreen,CC,1.47E-05,7.25,5.40,15,3195,cell periphery,1.26E-03
lightgreen,BP,2.38E-05,471.17,0.01,2,5,cobalt ion transport,1.34E-02
lightgreen,MF,4.22E-05,309.15,0.01,2,7,cobalamin binding,3.79E-03
magenta,CC,3.29E-04,3.39,31.31,43,7625,intracellular organelle,4.40E-02
magenta,CC,3.51E-04,3.37,31.38,43,7641,organelle,4.70E-02
magenta,CC,4.21E-04,4.53,36.84,47,8972,intracellular part,5.65E-02
magenta,BP,5.26E-04,78.28,0.04,2,8,regulation of centrosome cycle,3.31E-01
magenta,CC,5.77E-04,2.91,28.36,40,6906,intracellular membrane-bounded organelle,7.74E-02
magenta,CC,6.01E-04,2.90,28.40,40,6916,membrane-bounded organelle,8.05E-02
magenta,CC,8.90E-04,4.21,37.59,47,9154,intracellular,1.19E-01
pink,CC,2.43E-13,8.95,3.97,24,704,extracellular space,2.92E-11
pink,CC,3.65E-12,6.04,9.14,33,1621,extracellular region,4.38E-10
pink,MF,3.94E-12,16.53,1.12,14,186,cytokine activity,1.10E-09
pink,CC,5.52E-12,7.34,5.04,25,894,extracellular region part,6.62E-10
pink,MF,8.92E-09,12.55,1.08,11,180,cytokine receptor binding,2.50E-06
pink,BP,4.49E-08,5.64,4.50,19,772,defense response,4.50E-05
pink,MF,2.27E-07,28.39,0.27,6,44,chemokine activity,6.36E-05
pink,MF,3.87E-07,25.68,0.29,6,48,chemokine receptor binding,1.08E-04
pink,BP,2.69E-06,3.95,7.05,21,1211,immune system process,2.70E-03
pink,BP,7.19E-06,4.40,4.54,16,780,immune response,7.20E-03
purple,CC,1.73E-26,62.69,0.56,20,111,intermediate filament,2.51E-24
purple,CC,1.54E-24,48.65,0.69,20,137,intermediate filament cytoskeleton,2.23E-22
purple,CC,2.31E-11,7.92,4.09,22,806,cytoskeletal part,3.35E-09
purple,CC,9.80E-10,5.96,5.99,24,1181,cytoskeleton,1.42E-07
purple,BP,1.61E-06,30.60,0.20,5,56,negative regulation of endopeptidase activity,9.00E-04
purple,MF,5.95E-06,22.94,0.26,5,71,serine-type endopeptidase inhibitor activity,1.22E-03
purple,BP,1.14E-05,19.96,0.30,5,83,negative regulation of peptidase activity,6.36E-03
purple,BP,4.09E-05,15.08,0.39,5,108,regulation of proteolysis,2.29E-02
purple,CC,4.55E-05,3.05,10.63,24,2096,non-membrane-bounded organelle,6.59E-03
purple,CC,4.55E-05,3.05,10.63,24,2096,intracellular non-membrane-bounded organelle,6.59E-03
red,CC,5.07E-05,2.64,57.10,75,7625,intracellular organelle,1.21E-02
red,CC,5.60E-05,2.62,57.22,75,7641,organelle,1.34E-02
red,CC,5.65E-05,3.21,67.19,83,8972,intracellular part,1.35E-02
red,CC,7.02E-05,2.26,33.53,52,4478,organelle part,1.68E-02
red,CC,1.09E-04,2.21,33.09,51,4419,intracellular organelle part,2.61E-02
red,MF,1.19E-04,2.32,47.35,65,6043,protein binding,4.06E-02
red,CC,1.58E-04,2.31,51.72,69,6906,intracellular membrane-bounded organelle,3.77E-02
red,CC,1.67E-04,2.30,51.79,69,6916,membrane-bounded organelle,4.00E-02
red,CC,1.81E-04,2.98,68.55,83,9154,intracellular,4.32E-02
red,BP,2.06E-04,32.26,0.12,3,15,embryonic hindlimb morphogenesis,2.76E-01
salmon,BP,2.42E-07,47.72,0.14,5,67,biomineral tissue development,5.98E-05
salmon,CC,7.41E-06,5.87,3.92,14,1621,extracellular region,6.97E-04
salmon,CC,1.18E-04,176.91,0.02,2,7,voltage-gated sodium channel complex,1.11E-02
salmon,MF,2.49E-04,111.34,0.02,2,10,voltage-gated sodium channel activity,3.26E-02
salmon,CC,2.51E-04,110.54,0.02,2,10,sodium channel complex,2.36E-02
salmon,BP,4.44E-04,78.97,0.03,2,15,defense response to fungus,1.10E-01
salmon,BP,8.81E-04,54.00,0.04,2,21,killing of cells of other organism,2.18E-01
tan,CC,1.61E-04,4.63,2.47,10,432,ribonucleoprotein complex,2.37E-02
tan,BP,1.70E-04,190.95,0.02,2,4,selenocysteine incorporation,1.23E-01
tan,BP,1.70E-04,190.95,0.02,2,4,translational readthrough,1.23E-01
tan,CC,5.21E-04,3.28,52.33,64,9154,intracellular,7.66E-02
tan,CC,5.41E-04,3.67,3.42,11,598,nucleoplasm part,7.96E-02
tan,BP,5.91E-04,2.42,16.69,29,3100,gene expression,4.29E-01
tan,BP,7.69E-04,2.36,26.23,39,4871,cellular macromolecule metabolic process,5.58E-01
turquoise,BP,4.21E-11,2.44,42.06,86,388,sensory perception,2.07E-07
turquoise,CC,3.42E-10,1.62,178.69,255,1621,extracellular region,1.99E-07
turquoise,BP,1.98E-09,3.02,20.16,49,186,visual perception,9.71E-06
turquoise,BP,1.98E-09,3.02,20.16,49,186,sensory perception of light stimulus,9.71E-06
turquoise,BP,7.90E-08,9.70,2.82,14,26,phototransduction,3.88E-04
turquoise,CC,2.57E-06,1.67,77.60,117,704,extracellular space,1.50E-03
turquoise,BP,3.22E-06,6.12,3.58,14,33,detection of light stimulus,1.58E-02
turquoise,BP,5.17E-06,1.31,452.55,524,4175,multicellular organismal process,2.54E-02
turquoise,CC,5.74E-06,28.39,0.99,7,9,photoreceptor inner segment,3.34E-03
turquoise,CC,6.24E-06,8.13,2.43,11,22,high-density lipoprotein particle,3.63E-03
yellow,CC,4.49E-05,1.70,140.34,171,6916,membrane-bounded organelle,1.44E-02
yellow,CC,6.96E-05,1.67,140.13,170,6906,intracellular membrane-bounded organelle,2.23E-02
yellow,CC,2.40E-04,1.58,86.02,113,4239,nucleus,7.68E-02
yellow,CC,3.10E-04,1.75,185.75,209,9154,intracellular,9.92E-02
yellow,MF,4.08E-04,Inf,0.04,2,2,glutamate dehydrogenase activity,2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,glutamate dehydrogenase [NAD(P)+] activity,2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,"oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor",2.25E-01
yellow,MF,4.08E-04,Inf,0.04,2,2,leucine binding,2.25E-01
yellow,CC,4.77E-04,1.69,182.06,205,8972,intracellular part,1.53E-01
yellow,CC,5.66E-04,1.58,155.05,180,7641,organelle,1.81E-01
{csv}