User: Assa Yeroslaviz

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Assa Yeroslaviz1.4k
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Munich, Germany
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Posts by Assa Yeroslaviz

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Comment: C: Plot genes with similar expression patterns
... why not trying to cluster them based on their expression (heatmap, kmeans, SOM etc.) and than plot the separate groups. DESeq(2) was not meant for such results. ...
written 4 weeks ago by Assa Yeroslaviz1.4k
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Comment: C: Time-series analysis with DESeq2
... thank you for the time. ...
written 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months 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 3 months ago by Assa Yeroslaviz1.4k • updated 3 months ago by Michael Love23k
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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 3 months ago by Assa Yeroslaviz1.4k • updated 3 months ago by Michael Love23k

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