[R] Getting error in clustering analysis of RNAseq raw reads

[Yogesh Gupta]

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*

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