Yogesh Gupta
2016-Nov-03 12:43 UTC
[R] Getting error in clustering analysis of RNAseq raw reads
Dear All, I have raw read for around 40,000 transcripts at 3 development stages in four tissue with two biological replicate. I want to do clustering to see the correlation between biological replicate and tissue gene expression. For that I used the following cammand but geeting error at the end. Please suggest me how can I resolve this analysis or suggest some other to show the correlation through dendrogram bet tissue and replicates.> Tree=read.table("JiYoung_rawcount2.txt", header=T) > attach(Tree) > Tree=na.omit(Tree) > Tree1=Tree[,1:37]Error in `[.data.frame`(Tree, , 1:37) : undefined columns selected> Tree1=Tree[,1:34] > Tree1=scale(Tree1) > fit=kmeans(Tree1,6) > aggregate(Tree1,by=list(fit$cluster),FUN=mean)Group.1 X216_5W_Ca1 X216_5W_Ca2 X216_5W_Co1 X216_5W_CO2 X216_5W_Pa1 1 1 0.58858040 0.43817608 0.36369515 0.38041543 0.35233882 2 2 2.42908764 1.91210976 1.52605404 1.58443684 1.52558080 3 3 74.03474419 67.01505049 44.83518300 55.75108909 67.08145692 4 4 22.49829929 18.97402000 24.67343279 24.17280525 19.70225908 5 5 5.76673305 5.49181254 5.86183195 5.51501833 5.60290364 6 6 -0.08598393 -0.06821359 -0.05891407 -0.06141244 -0.05887959 X216_5W_Pa2 X216_7W_Ca1 X216_7W_Co1 X216_7W_Pa1 X216_7W_Pa2 X216_9W_Ca1 1 0.31858916 0.40034893 0.56150029 0.23379224 0.16387140 0.69427423 2 1.42676388 1.67809954 2.45417069 1.06859194 0.79864768 2.74500617 3 67.70121040 61.23933043 63.72713464 59.05530410 56.49776253 72.58425992 4 18.95159487 13.49035976 28.20156499 7.03145799 6.75403043 20.06947106 5 5.11737426 4.47486147 9.27074003 2.95413750 2.21762466 6.78433102 6 -0.05486169 -0.06000421 -0.08838463 -0.03861134 -0.02995435 -0.09670259 X216_9W_Ca2 X216_9W_Co1 X216_9W_Co2 X216_9W_Pa1 X216_9W_Pa2 X218_5W_Ca1 1 0.6912312 0.46185370 0.45662675 0.48050371 0.4102703 0.7362048 2 2.7313814 1.94074293 1.89761725 1.89666393 1.7667720 3.1811285 3 71.1276692 65.26586773 66.96323923 77.45296500 67.2184393 62.4966761 4 19.4695963 21.52139536 21.46531283 19.59961960 14.2639218 28.3129021 5 6.4045681 5.20213688 5.12189575 6.36399774 5.5607615 8.2983905 6 -0.0956101 -0.07048408 -0.06982468 -0.07355444 -0.0635680 -0.1064461 X218_5W_Ca2 X218_5W_Co1 X218_5W_Co2 X218_5W_Pa1 X218_5W_Pa2 X218_7W_Ca1 1 0.7562678 0.6313518 0.60735044 0.5181326 0.62021074 0.58441077 2 3.2286191 2.7650505 2.55823136 2.3362218 2.78896881 2.67308175 3 50.6247201 57.6083926 53.04016813 57.0939083 51.33990373 61.67671029 4 32.4676288 30.6562363 31.71334139 30.3348985 33.54598480 27.14293723 5 8.9548249 9.3425124 8.59189383 8.0038275 8.75233324 8.76179017 6 -0.1089077 -0.0963359 -0.09178966 -0.0826968 -0.09523603 -0.09085913 X218_7W_Ca2 X218_7W_Co1 X218_7W_Co2 X218_7W_Pa1 X218_7W_Pa2 X218_9W_Ca1 1 0.50019728 0.56001261 0.57024565 0.44437646 0.44479186 0.8400651 2 2.24049619 2.48926833 2.44390725 2.20582519 2.23325003 3.5810738 3 64.39243727 63.50454637 61.15957849 73.95971794 69.46363454 58.0319671 4 22.66822963 26.67150058 29.07678293 19.49939666 20.82222737 28.5564765 5 7.35115400 9.66796018 9.40071423 6.68316366 7.22795784 9.6139084 6 -0.07838953 -0.08849961 -0.08905063 -0.07339317 -0.07410584 -0.1185144 X218_9W_Ca2 X218_9W_Co1 X218_9W_Co2 X218_9W_Pa1 X218_9W_Pa2 1 0.7386879 0.64248657 0.64966599 0.49104422 0.54706215 2 3.1917475 2.75317071 2.82258034 2.24793860 2.56671355 3 63.5127116 53.12081116 57.05732779 62.67926202 67.64227975 4 27.5673337 27.47366571 25.77146680 20.28975742 20.37098419 5 8.7078573 8.37873305 8.67721724 5.92146810 6.84227840 6 -0.1070434 -0.09456489 -0.09594609 -0.07535101 -0.08380287> Tree1<-data.frame(Tree1,fit$cluster) > d=dist(Tree1,method="euclidean") > fit=hclust(d,method="ward.D2")*** caught segfault *** address 0x7f51c12c0228, cause 'memory not mapped' Traceback: 1: hclust(d, method = "ward.D2") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: Thanks *Yogesh Gupta* [[alternative HTML version deleted]]