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petitmingchang / TO-GCN

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data
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How do you code/order timepoints that have replicates? #4

Closed ckeeling closed 4 years ago

ckeeling commented 5 years ago

Hello again, I have 2 conditions at 5 timepoints, with 3 biological replicates/timepoint/condition (30 columns of data). How do I order or specify this experimental design? Your examples only indicate the number of samples in the two conditions, not the timepoints or replication. Thanks!

ckeeling commented 4 years ago

Is this possible to do @petitmingchang?

petitmingchang commented 4 years ago

Hi ckeeling,

Yes, two options you can try:

  1. Use each replicate as an individual sample, so there will be 15 samples for each condition.
  2. Use average value of three replicates for each time point, so there will be 5 samples for each condition. According to my experiences, the 2nd option makes more sense and usually has better result than the first one.
ckeeling commented 4 years ago

Thanks @petitmingchang

So, it is the assumption of the program that the time series is increasing with column left to right, for each condition, and it is categorical and not a continuous scale? I.e. Days 1, 2, 3 or 1, 5, 100 is not considered?

petitmingchang commented 4 years ago

Yes, you are right.

ckeeling commented 4 years ago

Thanks