User: indrik.wijaya

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Posts by indrik.wijaya

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Comment: C: DeSeq2 Ribosome Profiling: multiple factor design
... Hi, Mike, Okay, will do! Thanks so much for the help :) ...
written 8 weeks ago by indrik.wijaya • 10
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Comment: C: DeSeq2 Ribosome Profiling: multiple factor design
... 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 8 weeks ago by indrik.wijaya • 10
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Comment: C: Data preparation and Machine learning on time course RNAseq data
... 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 8 weeks ago by indrik.wijaya • 10
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Comment: C: DeSeq2 Ribosome Profiling: multiple factor design
... Hi Mike, Thanks for the reply, I want to compare both ie to t0 and ratio within each time point alone. ...
written 8 weeks ago by indrik.wijaya • 10
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DeSeq2 Ribosome Profiling: multiple factor design
... 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 ...
deseq2 design timeseries written 8 weeks ago by indrik.wijaya • 10 • updated 8 weeks ago by Michael Love ♦ 22k
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Comment: C: DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald
... Hi, Mike, thank you for the help and sorry for the basic question! I missed out the details from ?results.  ...
written 10 weeks ago by indrik.wijaya • 10
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Comment: C: DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald
... 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 10 weeks ago by indrik.wijaya • 10
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DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
... 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   ...
deseq2 wald lrt ribosome profiling written 10 weeks ago by indrik.wijaya • 10 • updated 10 weeks ago by Michael Love ♦ 22k

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