User: thindmarsmission

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Posts by thindmarsmission

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Comment: C: Deseq2 design for one condition over 8 different time point
... thanks, i got following combinations:(and sorry to bother you again) > resultsNames(dds)  [1] "Intercept"     "rep_a2_vs_a1"  "rep_a3_vs_a1"  "time_t2_vs_t1" "time_t3_vs_t1" "time_t4_vs_t1" "time_t5_vs_t1"  "time_t6_vs_t1" "time_t7_vs_t1" "time_t8_vs_t1" What is the meaning of "reduced=~rep" an ...
written 7 months ago by thindmarsmission0
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Comment: C: Deseq2 design for one condition over 8 different time point
... Thanks for your reply Michael, yes, in one case i have replicates across all time points, I used ~rep+time for full design and ~rep for reduced. I got following results > resultsNames(dds) [1] "Intercept" "rep"       "time"     Should not I get, like "t1_vs_t2" "t2_vs_t3" etc.. actually, I wan ...
written 7 months ago by thindmarsmission0
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Deseq2 design for one condition over 8 different time point
... HI! I have a question, about design matrix in Deseq2, when I don't have any control or conditions. But same sample at different time points for differential expression analysis . I want to do differential expression between different time points. How I should define my Design ? design(dds) <- ~ ...
deseq deseq2 rna-seq design matrix written 7 months ago by thindmarsmission0 • updated 7 months ago by Michael Love23k
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Comment: C: how to plot trends for differentialy expressed genes from normalized count matri
... Thank you, but for clustering the genes having similar trends throughout, what I can use ? I am new to this field.  sorry for stupid questions.   ...
written 7 months ago by thindmarsmission0
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how to plot trends for differentialy expressed genes from normalized count matrix (EdgeR)
... Hi!! I want to plot trends between genes across different conditions from my normalized count matrix (featurecount-EdgeR). I was using "csCluster" in cummerbund. Now I switched to this pipeline and I am wondering, if similar pacakage or tool is available for plotting those kinds of trends. eg : be ...
visualization clustering edger written 7 months ago by thindmarsmission0 • updated 7 months ago by James W. MacDonald50k

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