Entering edit mode
2.2 years ago
shome
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10
How to analyse RNA-seq data which has been stored over time ? For instance, if there are 6 samples collected from a individual over the course of three years and then we do the analysis.Do we normalize from time 0 through 36 months for each individual or do we compressing all the data to a mean.How to address the issue ?
You should take a look at the edgeR userguide. The answer may depend on the questions you want to ask of the data, and there are several examples in that guide of how to ask questions. For instance, will you be asking questions between individuals? Or between different time points? Or both? For some experiments, a comparison of interest might be too extreme (i.e. comparing an embryo to an adult), but if you have time points in between you can make successive comparisons, or find genes which change relative to the mean of the whole data set over time. Even so, regarding normalization specifically, it is common to put all the data together in a single table for Normalization. In your question you might be referring to normalization in the sense of making comparisons (rather than making all data sets comparable to each other).
You generally don't want to collapse samples unless they are technical replicates. What analysis you do will often depend on what data you have available and what questions you want to answer, so we would need to know more about your experiment and goals to give useful advice.
So,I think the data is like from one individual we would collect sample at months 6,12,18,24,30,36 and then analyse and similar we would do for multiple individuals.
What general information do you want to get from the data?