Hi All!!!
I am trying to draw a correlation heatmap for my RNA-seq data. I would like to input the whole transcriptome of each sample (n=20) and see the similarities of each dataset using pearson and spearman correlations.
I have some issues in running my script on R: I could do it for a small dataset (300 genes) but not for the whole transcriptome...it takes forever and simply doesn't produce anything after 20 minutes!
Can anyone help with this?
Thanks!
Manu
here is my script (for spearman):
`cumulus_cluster` <- read.csv("transcriptome_corr.csv")
data.raw<- `cumulus_cluster`
data<-data.matrix(data.raw)
genes<-data[,2:15220]
install.packages("gplots")
library("gplots")
data.corr<-cor(genes,method="spearman")
heatmap.2(data.corr)
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.4.1 ggplot2_1.0.1 edgeR_3.10.2 limma_3.24.13
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 digest_0.6.8 MASS_7.3-42 grid_3.2.1 plyr_1.8.3
[6] gtable_0.1.2 magrittr_1.5 scales_0.2.5 stringi_0.5-5 proto_0.3-10
[11] tools_3.2.1 stringr_1.0.0 munsell_0.4.2 colorspace_1.2-6
I am trying to draw a correlation heatmap for my RNA-seq data. I would like to input the whole transcriptome of each sample (n=20) and see the similarities of each dataset using pearson and spearman correlations.
I have some issues in running my script on R: I could do it for a small dataset (300 genes) but not for the whole transcriptome...it takes forever and simply doesn't produce anything after 20 minutes!
Can anyone help with this?
Thanks!
Manu
here is my script (for spearman):
`cumulus_cluster` <- read.csv("transcriptome_corr.csv")
data.raw<- `cumulus_cluster`
data<-data.matrix(data.raw)
genes<-data[,2:15220]
install.packages("gplots")
library("gplots")
data.corr<-cor(genes,method="spearman")
heatmap.2(data.corr)
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reshape2_1.4.1 ggplot2_1.0.1 edgeR_3.10.2 limma_3.24.13
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 digest_0.6.8 MASS_7.3-42 grid_3.2.1 plyr_1.8.3
[6] gtable_0.1.2 magrittr_1.5 scales_0.2.5 stringi_0.5-5 proto_0.3-10
[11] tools_3.2.1 stringr_1.0.0 munsell_0.4.2 colorspace_1.2-6
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