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User: Assa Yeroslaviz

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Assa Yeroslaviz1.4k
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Posts by Assa Yeroslaviz

<prev • 295 results • page 1 of 30 • next >
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Comment: C: Time-series analysis with DESeq2
... thank you for the time. ...
written 12 hours ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... Let's say I have this sample information condtion timepoint replicate group Sample_1 WT 0h 1 WT_0h Sample_2 WT 0h 2 WT_0h Sample_3 WT 0h 3 WT_0h Sample_4 WT 1h 1 WT_1h ... ...
written 13 hours ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... great. Is there an interaction where I can look for genes with significant changes in all time points? I mean a constant trend over all time points? ...
written 14 hours ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... great. Is there an interaction where I can look for genes with significant changes in all time points? I mean a constant trend over all time points> ...
written 14 hours ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... great. Is there an interaction where I can look for genes with significant changes in all time points? I mean a constant trendover all time points> ...
written 14 hours ago by Assa Yeroslaviz1.4k
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Comment: C: clarification of time-series analysis
... again thanks. It starts to becoming clearer. But than why should someone use the second design? Is there an event where **not controlling** for baseline differences is needed? ...
written 14 hours ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... thanks Michael for the fast response. so transferring it from the workflow, something like this should do it for me? ddsTC <- DESeqDataSet(counts, ~ strain + time + strain:time) ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ strain + time) Does this apply only for cases where I have ...
written 14 hours ago by Assa Yeroslaviz1.4k
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clarification of time-series analysis
... In [a great post previously answered by @Michael Love][1] I have found his response as such > "strainmut.minute15" is the difference between Mut vs WT at minute 15, **controlling for baseline**. If you add "strain_mut_vs_wt" to this, you get the LFC for Mutant vs WT at minute 15, not controlling ...
deseq2 lrt baseline written 14 hours ago by Assa Yeroslaviz1.4k • updated 14 hours ago by Michael Love22k
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Time-series analysis with DESeq2
... I was wondering how one can do a deseq2 analysis of multiple time points when trying to test for a WT vs TREAT difference at any of the given times. Let's say I have three time points (1h,2h,3h) and two conditions (WT, TREAT) In edgeR one can create a contrast matrix and pass the complete matrix t ...
edger deseq2 design matrix time-series written 14 hours ago by Assa Yeroslaviz1.4k • updated 14 hours ago by Michael Love22k
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differentail expression analysis with interaction terms
... Hi, I'm working with a data set with three time points (1d, 5d, 10d and four treatments + ctrl treat1, treat2, treat3, treat4). For each of the 15 combinations I have triplicates (in total 45) If I understood it correctly both edger and deseq2 works with this interactions terms to combine multipl ...
edger deseq2 design matrix interaction written 4 days ago by Assa Yeroslaviz1.4k • updated 4 days ago by James W. MacDonald49k

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