Hi Douglas,
I encourage you and anyone else that has encountered this error to up-vote this issue in the Galaxy Trello board:
That will help us prioritize work. Thanks for reporting this.
Dave C
On Thu, Jan 30, 2014 at 10:24 AM, Douglas Cavener drc9@psu.edu wrote:
I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered by Galaxy. Looks like the negative exponent is ignored and so if you sorting something like P values (see example below) then you find these ordered above P=1 instead at the other end of the list where P is near zero. In the example below a KEGG list is ordered on column 5 in asending order by galaxy. If you scroll to the bottom of the list, however, you will see the smallest numbers all of which are in scientific notation. I should note that I can can copy this into excel and excel will properly sort scientific notation. So this seems to be a specific problem with Galaxy. I found this problem with both filtering and sorting functions of Galaxy. Doug Cavener
410.53261.00.0000025cfa04146=Peroxisome390.5325 1.00.0000038cfa04640=Hematopoietic cell lineage290.59131.00.0000044cfa00980=Metabolism of xenobiotics by cytochrome P450 220.63101.00.000016cfa00140=Steroid hormone biosynthesis28 0.56191.00.000027cfa05204=Chemical carcinogenesis 110.8531.00.000033cfa00511=Other glycan degradation250.57161.00.000052cfa00600=Sphingolipid metabolism 9 0.9021.00.000074cfa00740=Riboflavin metabolism230.58141.00.000079cfa00380=Tryptophan metabolism 150.6861.00.000096cfa04977=Vitamin digestion and absorption22 0.56171.00.00017cfa00071=Fatty acid metabolism 220.56171.00.00017cfa05150=Staphylococcus aureus infection260.53271.00.00017cfa00982=Drug metabolism - cytochrome P450 490.44421.00.00018cfa04142=Lysosome560.42471.00.00024cfa04630=Jak-STAT signaling pathway 340.48351.00.00026cfa03320=PPAR signaling pathway130.685 1.00.00027cfa00531=Glycosaminoglycan degradation 200.56211.00.00043cfa04975=Fat digestion and absorption220.54241.00.00043cfa00830=Retinol metabolism 19 0.56201.00.00053cfa00565=Ether lipid metabolism140.61111.00.00092cfa00591=Linoleic acid metabolism 200.53281.00.0011cfa02010=ABC transporters220.50321.0 0.0015cfa00280=Valine, leucine and isoleucine degradation 330.44441.0 0.0020cfa04974=Protein digestion and absorption150.56211.00.0022cfa03440=Homologous recombination 140.56191.00.0028cfa00650=Butanoate metabolism350.42481.0 0.0035cfa05323=Rheumatoid arthritis 160.52311.00.0043cfa00350=Tyrosine metabolism160.52311.00.0043cfa05320=Autoimmune thyroid disease 120.57151.0 0.0044cfa00592=alpha-Linolenic acid metabolism150.52301.00.0054cfa00760=Nicotinate and nicotinamide metabolism 210.47391.00.0054cfa05144=Malaria840.36661.0 0.0059cfa04080=Neuroactive ligand-receptor interaction 160.48331.00.0091cfa05143=African trypanosomiasis120.52291.00.011cfa00340=Histidine metabolism 140.48340.99 0.015cfa05330=Allograft rejection90.56181.00.015cfa04614=Renin-angiotensin system 31.011.00.021cfa00780=Biotin metabolism350.38560.990.021cfa00240=Pyrimidine metabolism15 0.44430.990.030cfa04940=Type I diabetes mellitus110.48360.99 0.032cfa00563=Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 290.38 540.980.032cfa04512=ECM-receptor interaction200.41500.980.034cfa04622=RIG-I-like receptor signaling pathway 90.50320.990.037cfa00100=Steroid biosynthesis10 0.48370.990.042cfa04950=Maturity onset diabetes of the young 70.54230.99 0.042cfa03450=Non-homologous end-joining60.55220.990.055cfa00430=Taurine and hypotaurine metabolism 60.55220.990.055cfa00790=Folate biosynthesis22 0.38580.970.060cfa05140=Leishmaniasis 120.43460.970.062cfa00512=Mucin type O-Glycan biosynthesis30.7540.990.068cfa00061=Fatty acid biosynthesis 30.7540.990.068cfa00232=Caffeine metabolism230.37620.960.070cfa04115=p53 signaling pathway 290.36640.960.071cfa00564=Glycerophospholipid metabolism 80.47380.980.071cfa00120=Primary bile acid biosynthesis 200.38590.960.074cfa00561=Glycerolipid metabolism190.38570.960.076cfa04612=Antigen processing and presentation 48 0.34740.950.076cfa05152=Tuberculosis180.38530.960.077cfa00510=N-Glycan biosynthesis 21.011.00.077cfa00290=Valine, leucine and isoleucine biosynthesis160.39520.960.079cfa00500=Starch and sucrose metabolism 160.39 520.960.079cfa04621=NOD-like receptor signaling pathway120.41490.960.080cfa00410=beta-Alanine metabolism 70.47390.970.093cfa00604=Glycosphingolipid biosynthesis - ganglio series330.34720.940.094cfa05146=Amoebiasis 80.44410.960.097cfa00900=Terpenoid backbone biosynthesis40.57150.980.099cfa00460=Cyanoamino acid metabolism 4 0.57150.980.099cfa00750=Vitamin B6 metabolism120.40510.950.10cfa00052=Galactose metabolism 120.40510.950.10cfa00983=Drug metabolism - other enzymes90.4346 0.960.10cfa00040=Pentose and glucuronate interconversions 50.50320.970.11cfa04122=Sulfur relay system260.35700.930.12cfa04064=NF-kappa B signaling pathway 100.4051 0.940.13cfa05332=Graft-versus-host disease170.36630.920.13cfa00480=Glutathione metabolism 210.35680.920.13cfa05133=Pertussis70.44450.950.13cfa00770=Pantothenate and CoA biosynthesis 120.38610.920.15cfa03410=Base excision repair210.3471 0.900.15cfa04976=Bile secretion15 0.36650.900.16cfa04978=Mineral absorption40.50320.960.16cfa00072=Synthesis and degradation of ketone bodies 500.32780.880.16cfa00230=Purine metabolism80.40510.930.16 cfa05310=Asthma60.43 460.940.17cfa00603=Glycosphingolipid biosynthesis - globo series20.6780.980.19cfa00785=Lipoic acid metabolism 80.38550.900.20cfa00062=Fatty acid elongation80.38550.900.20cfa03430=Mismatch repair11 0.35670.880.22cfa05340=Primary immunodeficiency120.34730.850.25cfa00260=Glycine, serine and threonine metabolism 400.31810.810.25cfa04145=Phagosome420.31820.800.25cfa05164=Influenza A130.33 750.830.27cfa00970=Aminoacyl-tRNA biosynthesis11.011.00.28cfa00472=D-Arginine and D-ornithine metabolism4 0.40510.890.29cfa00130=Ubiquinone and other terpenoid-quinone biosynthesis40.40510.890.29cfa00920=Sulfur metabolism 8 0.35690.840.29cfa00630=Glyoxylate and dicarboxylate metabolism360.30850.76 0.30cfa04514=Cell adhesion molecules (CAMs) 100.33750.810.31cfa00640=Propanoate metabolism20.50320.930.31cfa00730=Thiamine metabolism 70.35680.840.31cfa01040=Biosynthesis of unsaturated fatty acids140.32770.780.32cfa05134=Legionellosis 440.3086 0.740.32cfa05168=Herpes simplex infection110.32760.790.33cfa00860=Porphyrin and chlorophyll metabolism 120.32790.770.36cfa00620=Pyruvate metabolism31 0.30870.700.38cfa05145=Toxoplasmosis 60.33750.790.38cfa00670=One carbon pool by folate120.31810.730.39cfa04672=Intestinal immune network for IgA production 120.31810.730.39cfa04973=Carbohydrate digestion and absorption 140.30840.720.40cfa00520=Amino sugar and nucleotide sugar metabolism 11 0.31830.720.41cfa05219=Bladder cancer230.29880.690.41cfa05222=Small cell lung cancer 80.31810.720.44cfa00601=Glycosphingolipid biosynthesis - lacto and neolacto series80.31810.720.44cfa04966=Collecting duct acid secretion 50.31800.730.47cfa00533=Glycosaminoglycan biosynthesis - keratan sulfate10.50320.920.48cfa00300=Lysine biosynthesis 100.29890.67 0.48cfa03030=DNA replication120.29900.620.51cfa04930=Type II diabetes mellitus 330.28920.570.51cfa04110=Cell cycle160.28910.590.53cfa05416=Viral myocarditis2 0.33750.790.53cfa00400=Phenylalanine, tyrosine and tryptophan biosynthesis240.28930.570.53cfa04972=Pancreatic secretion 50.29 890.680.53cfa00360=Phenylalanine metabolism130.27940.530.59cfa00310=Lysine degradation 80.27950.540.62cfa00250=Alanine, aspartate and glutamate metabolism80.27950.540.62cfa00514=Other types of O-glycan biosynthesis 4 0.27950.590.63cfa00450=Selenocompound metabolism40.27950.590.63cfa01210=2-Oxocarboxylic acid metabolism 110.26970.490.64cfa04330=Notch signaling pathway140.2696 0.490.64cfa00330=Arginine and proline metabolism 40.251000.530.69cfa00053=Ascorbate and aldarate metabolism80.251000.450.70cfa00270=Cysteine and methionine metabolism 90.251000.440.70cfa04623=Cytosolic DNA-sensing pathway180.2598 0.390.71cfa04210=Apoptosis 50.241070.450.73cfa04140=Regulation of autophagy140.241040.330.77cfa00010=Glycolysis / Gluconeogenesis 70.23111 0.380.77cfa05020=Prion diseases80.241090.370.77cfa00051=Fructose and mannose metabolism 280.251010.280.79cfa04380=Osteoclast differentiation1 0.201290.580.80cfa00524=Butirosin and neomycin biosynthesis 60.221160.35 0.80cfa05216=Thyroid cancer310.251020.250.81cfa05012=Parkinson's disease 150.231100.270.82cfa04920=Adipocytokine signaling pathway160.241090.270.82cfa04350=TGF-beta signaling pathway 230.241050.240.82cfa05142=Chagas disease (American trypanosomiasis)90.221140.290.82cfa03420=Nucleotide excision repair 170.23 1120.240.83cfa05410=Hypertrophic cardiomyopathy (HCM)350.241030.220.83cfa05202=Transcriptional misregulation in cancer 100.221160.260.84cfa05014=Amyotrophic lateral sclerosis (ALS)130.221150.230.85cfa04370=VEGF signaling pathway 260.24108 0.200.86cfa05160=Hepatitis C310.241060.190.86cfa00190=Oxidative phosphorylation 760.25990.170.86cfa04151=PI3K-Akt signaling pathway70.21 1270.240.87cfa04742=Taste transduction 150.221180.180.88cfa05218=Melanoma 140.221220.170.90cfa05412=Arrhythmogenic right ventricular cardiomyopathy (ARVC) 170.221200.150.90cfa05414=Dilated cardiomyopathy40.181400.230.90cfa00534=Glycosaminoglycan biosynthesis - heparan sulfate / heparin 50.191360.200.90cfa00030=Pentose phosphate pathway210.221170.130.91cfa04726=Serotonergic synapse 150.21124 0.130.92cfa03008=Ribosome biogenesis in eukaryotes40.171450.190.92cfa04320=Dorso-ventral axis formation 70.191340.160.92cfa04960=Aldosterone-regulated sodium reabsorption220.221210.100.93cfa04066=HIF-1 signaling pathway 240.22119 0.110.93cfa04670=Leukocyte transendothelial migration280.221160.100.93cfa05161=Hepatitis B 430.231130.0950.93cfa04144=Endocytosis140.201280.110.94cfa05220=Chronic myeloid leukemia 50.171460.150.94cfa04744=Phototransduction60.181420.13 0.94cfa04130=SNARE interactions in vesicular transport 120.191330.0790.96cfa05211=Renal cell carcinoma230.211250.0670.96cfa05162=Measles4 0.151540.110.96cfa03020=RNA polymerase100.181410.0630.97cfa00562=Inositol phosphate metabolism4 0.14 1610.0790.97cfa04710=Circadian rhythm100.171460.0470.98cfa05210=Colorectal cancer150.18 1390.0340.98cfa04914=Progesterone-mediated oocyte maturation 200.191330.0280.98cfa04270=Vascular smooth muscle contraction 400.21123 0.0320.98cfa04510=Focal adhesion80.161500.0480.98cfa05213=Endometrial cancer10 0.151540.0150.99cfa05212=Pancreatic cancer100.161490.0290.99cfa04260=Cardiac muscle contraction10 0.161530.0210.99cfa05214=Glioma130.161510.0120.99cfa05215=Prostate cancer140.17148 0.0160.99cfa04012=ErbB signaling pathway140.181440.0250.99cfa04620=Toll-like receptor signaling pathway150.17 1460.0170.99cfa04650=Natural killer cell mediated cytotoxicity170.181430.0140.99cfa04114=Oocyte meiosis24 0.18137 0.0100.99cfa04910=Insulin signaling pathway320.201300.0150.99cfa05010=Alzheimer's disease 330.201310.0100.99cfa05016=Huntington's disease80.151580.0200.99cfa04730=Long-term depression 90.151570.0160.99cfa03018=RNA degradation90.151570.0160.99cfa04664=Fc epsilon RI signaling pathway 00.02040.381.0cfa00471=D-Glutamine and D-glutamate metabolism10.0362010.00141.0cfa00020=Citrate cycle (TCA cycle) 10.0451980.00761.0cfa03060=Protein export10.0531960.0181.0cfa04964=Proximal tubule bicarbonate reclamation 10.0591940.0301.0cfa00532=Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate100.131710.0017 1.0cfa04912=GnRH signaling pathway100.131720.00141.0cfa04070=Phosphatidylinositol signaling system100.14163 0.00531.0cfa05100=Bacterial invasion of epithelial cells110.0871861.6E-71.0cfa04310=Wnt signaling pathway110.13 1700.00121.0cfa04666=Fc gamma R-mediated phagocytosis110.151560.00871.0cfa04970=Salivary secretion13 0.0831871.9E-91.0cfa05034=Alcoholism130.131670.000671.0cfa04660=T cell receptor signaling pathway15 0.121730.0000581.0cfa04360=Axon guidance 150.121730.0000581.0cfa04530=Tight junction150.12 1750.0000101.0cfa04390=Hippo signaling pathway150.141640.000651.0cfa04722=Neurotrophin signaling pathway18 0.131690.0000421.0cfa03010=Ribosome180.141650.000151.0cfa04120=Ubiquitin mediated proteolysis18 0.161520.00351.0cfa05322=Systemic lupus erythematosus20.0162038.1E-151.0cfa03040=Spliceosome2 0.0282023.3E-81.0cfa03015=mRNA surveillance pathway260.191350.00881.0cfa03013=RNA transport270.15 159 0.0000191.0cfa05203=Viral carcinogenesis280.171450.00181.0cfa04141=Protein processing in endoplasmic reticulum 280.171480.000871.0cfa04062=Chemokine signaling pathway290.171470.000941.0cfa05169=Epstein-Barr virus infection 30.0382005.6E-81.0cfa04727=GABAergic synapse30.0521970.0000141.0cfa04720=Long-term potentiation 30.0671890.000451.0cfa04961=Endocrine and other factor-regulated calcium reabsorption30.0701880.000761.0 cfa04962=Vasopressin-regulated water reabsorption30.0911840.00901.0cfa05033=Nicotine addiction300.15155 0.000038 1.0cfa04810=Regulation of actin cytoskeleton310.181380.00401.0cfa04020=Calcium signaling pathway340.14160 0.00000111.0cfa04010=MAPK signaling pathway4 0.0611920.0000101.0cfa04971=Gastric acid secretion40.098 1820.00501.0cfa03022=Basal transcription factors460.191320.00171.0cfa05166=HTLV-I infection50.043 199 6.9E-111.0cfa04728=Dopaminergic synapse50.0561951.4E-71.0cfa04723=Retrograde endocannabinoid signaling5 0.0621900.00000111.0cfa04540=Gap junction50.11 1770.00821.0cfa05030=Cocaine addiction50.11 1800.00661.0 cfa03050=Proteasome50.121750.0101.0cfa04340=Hedgehog signaling pathway6 0.059193 3.4E-81.0cfa04725=Cholinergic synapse60.0611917.4E-81.0cfa04724=Glutamatergic synapse60.10181 0.00121.0cfa05031=Amphetamine addiction60.121740.00841.0cfa05217=Basal cell carcinoma60.121760.0045 1.0cfa05223=Non-small cell lung cancer620.21 1260.00381.0cfa05200=Pathways in cancer660.141621.1E-11 1.0cfa04740=Olfactory transduction70.111780.00161.0cfa04520=Adherens junction70.131660.0121.0 cfa05221=Acute myeloid leukemia80.0901850.0000141.0cfa04713=Circadian entrainment80.090 1850.0000141.0 cfa04916=Melanogenesis80.0951830.0000441.0cfa05032=Morphine addiction80.111790.000751.0cfa05132=Salmonella infection 80.131680.00681.0cfa04150=mTOR signaling pathway80.131680.00681.0cfa04721=Synaptic vesicle cycle 90.14161 0.00951.0cfa04662=B cell receptor signaling pathway320.6871.01.2E-8cfa03460=Fanconi anemia pathway 340.6491.04.2E-8cfa00590=Arachidonic acid metabolism850.45 401.04.9E-7cfa04060=Cytokine-cytokine receptor interaction 340.60121.0 5.3E-7cfa04610=Complement and coagulation cascades4080.38601.08.6E-11cfa01100=Metabolic pathways
--
Douglas R. Cavener Professor and Head Department of Biology 110 Life Science Building Pennsylvania State University University Park, PA 16802
(814) 865-4562 Dept Office (814) 865-9790 Lab Office (814) 865-9131 Fax drc9@psu.edu
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