Hello,
I have been using the following for smaller datasets and now suddenly for a larger data set it is not working. I haven't changed the formatting so I am not sure why. Is it too large data for the system? I am using values from half a matrix which is 534x534
The error is received when Running:
"dendrogram2=hclust(distance2,method="average")"
The error reads:
" Error: unexpected symbol in: "distance2=distance
dendrogram3=hclust(distance3,method="average "
Thanks,
-New to R
distance=structure(c(A2,B2,C2,D2,E2,F2,G2,H2,I2,J2,K2,L2,M2,N2,O2,P2,Q2,R2,S2,T2,U2,V2,W2,X2,Y2,Z2,AA2,BB2,CC2,DD2,EE2,FF2,GG2,HH2,II2,JJ2,KK2,LL2,MM2,NN2,OO2,PP2,QQ2,RR2,SS2,TT2,UU2,VV2,WW2,XX2,YY2,ZZ2,AAA2,BBB2,CCC2,DDD2,EEE2,FFF2,GGG2,HHH2,III2,JJJ2,KKK2,LLL2,MMM2,NNN2,OOO2,PPP2,QQQ2,RRR2,SSS2,TTT2,UUU2,VVV2,WWW2,XXX2,YYY2,ZZZ2,AAAA2,BBBB2,CCCC2,DDDD2,EEEE2,FFFF2,GGGG2,HHHH2,IIII2,JJJJ2,KKKK2,LLLL2,MMMM2,NNNN2,OOOO2,PPPP2,QQQQ2,RRRR2,SSSS2,TTTT2,UUUU2,VVVV2,WWWW2,XXXX2,YYYY2,ZZZZ2,AAAAA2,BBBBB2,CCCCC2,DDDDD2,EEEEE2,FFFFF2,GGGGG2,HHHHH2,IIIII2,JJJJJ2,KKKKK2,LLLLL2,MMMMM2,NNNNN2,OOOOO2,PPPPP2,QQQQQ2,RRRRR2,SSSSS2,TTTTT2,UUUUU2,VVVVV2,WWWWW2,XXXXX2,YYYYY2,ZZZZZ2,AAAAAA2,BBBBBB2,CCCCCC2,DDDDDD2,EEEEEE2,FFFFFF2,GGGGGG2,HHHHHH2,IIIIII2,JJJJJJ2,KKKKKK2,LLLLLL2,MMMMMM2,NNNNNN2,OOOOOO2,PPPPPP2,QQQQQQ2,RRRRRR2,SSSSSS2,TTTTTT2,UUUUUU2,VVVVVV2,WWWWWW2,XXXXXX2,YYYYYY2,ZZZZZZ2,AAAAAAA2,BBBBBBB2,CCCCCCC2,DDDDDDD2,EEEEEEE2,FFFFFFF2,GGGGGGG2,HHHHHHH2,IIIIIII2,JJJJJJJ2,KKKKKKK2,LLLLLLL2,MMMMMMM2,NNNNNNN2,OOOOOOO2,PPPPPPP2,QQQQQQQ2,RRRRRRR2), Size=534L, Labels=(c("1D1T","1DLI","1EZ4","1F8F","1GPD","1HSO","1ICI","1JKF","1KAE","1KEP","1LDM","1LLQ","1M2W","1NBO","1NHW","1PJS","1PZH","1QR6","1QRR","1R66","1U7H","1XCB","2DT5","2G82","2LDB","2O2S","2O2Y","2Q1T","2WDZ","3AW9","3BTS","3CEA","3GEG","3GFB","3HQ4","3JV7","3KEO","3LU1","3NRC","3OIF","3OJL","3PYM","3QBD","3QV1","3QVS","3R3S","3RFX","3RIY","3RU7","3SXP","3T4E","3TNL","3U31","3V1U","3VPS","3WMX","3WR5","4DL9","4FN4","4I5I","4JLW","4K28","4LRS","4M87","4MIY","4ND1","4NJO","4NR0","4NU5","4PZD","4Q3C","4QX6","4RQU","4TKM","4Z0H","5DDI","5ENV","5X20","3E18","2E37","1A5Z","1A9Y","1AHH","1B14","1B3R","1B8U","1BW9","1BXK","1CDO","1D7O","1DC6","1DQS","1DRU","1DSS","1E3L","1E6W","1EBF","1EE2","1EE9","1EK5","1EMD","1EVJ","1FDV","1FK8","1GCO","1GD1","1GEG","1GR0","1GUZ","1GY8","1H94","1HDG","1HDR","1HDY","1HKU","1HLP","1HWY","1HYH","1IB0","1J49","1J5P","1JQ5","1K4M","1KOL","1KQN","1LI4","1LLD","1LLU","1LW7","1M8K","1NFF","1NVM","1O5I","1OC4","1PJC","1QSG","1R37","1S7G","1SB8","1T24","1T2F","1UP6","1V8B","1V9L","1VC2","1VI2","1VJT","1VKO","1VM6","1W1U","1WDK","1WXH","1WZE","1X0X","1X1T","1XAG","1Y9E","1YBA","1Z45","1ZBQ","2A5F","2A9K","2AG5","2B4R","2B69","2C20","2C54","2CZC","2D1Y","2D8A","2DC1","2DFD","2DPH","2DVM","2EER","2EJV","2EKL","2EP7","2G5C","2G76","2GRU","2GSD","2HAE","2I65","2I9P","2IXA","2IZZ","2NAD","2NSY","2O23","2O2Z","2OME","2PD3","2PH5","2Q2Q","2QG4","2QJO","2V7G","2VHX","2VT2","2VZL","2W2L","2WYV","2XXJ","2YQ5","2YY7","2ZIZ","3A1N","3A28","3ABI","3B1J","3B6J","3C7A","3CIN","3CLH","3COS","3CPS","3D4P","3D64","3DMT","3DOC","3EC7","3ENK","3F3S","3F4B","3G1U","3GGG","3GNQ","3GVH","3GVP","3H9U","3HAD","3HDH","3HJA","3HL0","3HMQ","3I9K","3IJR","3JSA","3JYO","3JZD","3K31","3L0D","3M6I","3N58","3N7U","3NDR","3O9Z","3OA2","3OET","3OKF","3OND","3OX4","3P2O","3PGX","3PQD","3PVZ","3PXX","3Q3C","3QJ5","3RF7","3RSG","3S2E","3S55","3STH","3SX2","3SYT","3T7C","3UHA","3UVE","3W2E","3WLE","3WSW","3ZCX","3ZOK","4A7P","4B79","4BBJ","4BUZ","4BV3","4CPD","4CQL","4CR8","4GLL","4GLO","4GX2","4I1I","4ID9","4IIN","4K9D","4KUG","4L0Q","4L2I","4LIS","4LSM","4LVC","4MDH","4MP6","4NBT","4NBW","4NK5","4O59","4OHU","4P8R","4PLP","4RGB","4RMG","4URF","4WEC","4WNI","4WSO","4XR9","4XYE","4YR9","4ZGS","4ZQG","4ZVV","5AXA","5BSF","5DBG","5DN9","5DT9","5EJ2","5EKS","5F23","5F5N","5HA5","5HS6","5HVN","5IG2","5ILG","5JLA","5JY1","5JYD","5K4Q","5K8C","5L78","5MH6","5NUE","5OIC","5T57","5T5Q","5T8K","5TC4","5TEJ","5TRT","5TS3","5U4Q","5UJK","5US6","5V96","5VLD","5VN2","5VP5","5XTG","5Y1E","5Y8H","5YCR","5YSS","5ZZ6","6AA8","6ACH","6APH","6BWL","6C4J","6C8Q","6CEP","6DNT","6DUX","6F3M","6FG0","6GBN","6GSD","6H0P","6HLA","6ISV","6ITK","6IUN","6IWL","6K0G","6K13","6KTL","6KV9","6N7L","6OW4","6Q1Y","6R8G","6S49","6TQH","6UJK","6UK3","6VLO","6YEI","9LDT","1OBB","5GWT","6UH2","3NT2","4PLC","1U28","2BRU1","2BRU2","1A7A","1A7K","1BDB","1DHR","1DXY","1EJ2","1EVZ","1G1A","1GUY","1GV0","1IY8","1J0X","1K6X","1KVS","1KYQ","1LC3","1LRK","1LSS","1M76","1M8J","1MUU","1NUU","1OMO","1ORR","1PL6","1RKX","1SC6","1SOW","1U8X","1UR5","1UWK","1UWL","1WWK","1X87","1Y3I","1YWG","1Z0Z","1ZEM","1ZJZ","2BI4","2CFC","2EKP","2EWM","2FKN","2GDZ","2HDH","2HSD","2HUN","2I29","2JJY","2O4C","2P5U","2PD6","2PLA","2PV7","2PZK","2Q1W","2X0N","2Y99","3B1F","3B82","3EHE","3EYW","3H9E","3ICP","3KB6","3M2T","3NTQ","3ORF","3PTZ","3QVW","3QW2","3RUA","3TSC","3UKO","3UXY","3V1Y","3VPH","3W8D","3WDS","3WYE","3ZW9","4C4O","4E13","4EUF","4FBG","4GH5","4GKV","4IS3","4J9U","4KQX","4OM8","4PFJ","4PRL","4TWR","4WUV","4XGI","4XGN","4XKJ","4YWJ","4ZA2","4ZJU","4ZRM","5BR4","5C7O","5CEE","5COQ","5CP8","5GWR","5GY7","5JE8","5KOI","5TF4","5TPR","5Z75","5ZI2","6BI4","6C5C","6D9Y","6F9Q","6H9S","6IHD","6ITL","6IXM","6JYG","6QHE","6RQA","6S72","6WJ9","4J1T1","4J1T2","4LCE")), Diag=FALSE, Upper=FALSE, class="dist")
distance2=distance
dendrogram2=hclust(distance2,method="average")
plot(dendrogram2,main="NAD+ Binding Proteins",sub="MOE Generated Protein Alignment",ylab="% Dissimilarity",xlab="Pairwise Primary Structure Comparison",family="serif",cex.main=2, cex=0.6)