User: indrik.wijaya
indrik.wijaya • 20
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Posts by indrik.wijaya
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... Hi, Mike,
Okay, will do! Thanks so much for the help :) ...
written 11 months ago by
indrik.wijaya • 20
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... Hi Mike,
Thank for the help! I'm sorry if I want to clarify other things. I ran the it with design `~ time + assay + cond + cond:assay + time:assay + time:cond + time:cond:assay` as you suggested. I changed 'cyto' to 'a' and 'crude' to 'b' for simplicity. This is the resultsNames that I get
> ...
written 11 months ago by
indrik.wijaya • 20
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... You can take a look at this paper that gives a good summary on the different methods used for time-series gene expression data
https://www.nature.com/articles/nrg3244
Personally, I've tried using STEM (to cluster time-series), which can be easily downloaded from its homepage. Nonetheless, tradition ...
written 11 months ago by
indrik.wijaya • 20
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... Hi Mike,
Thanks for the reply, I want to compare both ie to t0 and ratio within each time point alone. ...
written 11 months ago by
indrik.wijaya • 20
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... Hi all, I am planning to run differential gene expression analysis with this kind of design matrix (4 time points, 2 replicates each, 2 different assays and 2 different types):
> sample_name time assay type
> rna_0_r1 t0 rna cyto
> rna_1_r1 t1 rna cyto
> rna_2_r1 t2 rn ...
written 11 months ago by
indrik.wijaya • 20
• updated
11 months ago by
Michael Love ♦ 26k
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... Hi, Mike, thank you for the help and sorry for the basic question! I missed out the details from ?results.
...
written 11 months ago by
indrik.wijaya • 20
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... Hi Mike, thank you for the reply. I apologize for not including this section from your reply that can be found here https://support.bioconductor.org/p/82614/ where you said that
They really give very similar inference. I think the difference in a few genes you are seeing is because of the fold ch ...
written 11 months ago by
indrik.wijaya • 20
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... Hi all, I'm running differential expression analysis on Ribosome Profiling Time-series data (ie I would like to study differences in translational efficiencies at different time points).
My design matrix looks something like this:
sample_name time assay
rna_0_r1 t0 rna
rna_1_r1 t1 ...
written 11 months ago by
indrik.wijaya • 20
• updated
11 months ago by
Michael Love ♦ 26k
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