Hi Douglas, I encourage you and anyone else that has encountered this error to up-vote this issue in the Galaxy Trello board:
https://trello.com/c/QZlmb0Yf That will help us prioritize work. Thanks for reporting this. Dave C On Thu, Jan 30, 2014 at 10:24 AM, Douglas Cavener <d...@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 > d...@psu.edu > > > > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
