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Old 05-28-2014, 12:24 AM   #1
ngs06
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Default Expression patterns from rna-seq data

Hi,
I would like to analyse single cell rna-seq data. The dataset contains 21000 genes and 98 samples. I would like to look at the samples and genes behaviours, like which group of samples have similar expression and also which group of genes have similar expression levels. I thought making the gene-wise and samplewise clustering and viewing them in a heatmap could give better picture to start with initial data analysis.
But the dimensions of the dataset are too huge, I am not able to plot the heatmaps in R.
Do anyone have suggestions regarding how to start with initial data analysis to look for the expression patterns in dataset.


MAny thanks!

Last edited by ngs06; 05-28-2014 at 12:27 AM.
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Old 05-28-2014, 12:55 AM   #2
mikep
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There's alot of noise in single cell RNA-seq. You are unlikely to get anything decent if you use the entire dataset, I'd recommend at least a count cut off, or as alot of people do use the genes associated with the first 2 principal components.

Anyway, for viz try TM4
http://www.tm4.org/
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Old 05-28-2014, 07:12 AM   #3
ngs06
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Quote:
Originally Posted by mikep View Post
There's alot of noise in single cell RNA-seq. You are unlikely to get anything decent if you use the entire dataset, I'd recommend at least a count cut off, or as alot of people do use the genes associated with the first 2 principal components.

Anyway, for viz try TM4
http://www.tm4.org/
Thanks for your suggestion. I do PCA, which seems to be much followed method for data reduction.
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