User: glados

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glados0
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Posts by glados

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Comment: C: DESeq2 unequal sample sizes
... Thank you very much for the advice. Are you saying I should put all three treatment groups into this formula? DESeq(ddsTC, test="LRT", reduced = ~ treatment + time) I understand that significant genes from this LRT will show those that changed during some time point in one of the groups, but it j ...
written 6 weeks ago by glados0
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Comment: C: DESeq2 unequal sample sizes
... Sure, I have edited the post now, but I don't think the time points are really relevant to the question, so in order to keep it simple I only mentioned the groups. Since A and B are two very different treatments I need to analyse them separately and describe their results separately. In the end I wa ...
written 6 weeks ago by glados0
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Comment: C: DESeq2 unequal sample sizes
... Sure, but that doesn't make sense in my case since A and B are very different and I have several time points as well. So I need to analyse A vs Ctrl separately over time, and then B vs Ctrl separately over time. These two analyses will be my main results. How A and B compare to the controls. Only in ...
written 6 weeks ago by glados0
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Comment: C: DESeq2 unequal sample sizes
... A and B are two different treatments with different individuals. A vs Ctrl will tell me which genes are different in treatment A, and B vs Ctrl will tell me which genes are different in treatment B.  I expect (and do get) quite different results from the two treatments, i.e. A vs Ctrl provides lots ...
written 6 weeks ago by glados0
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DESeq2 unequal sample sizes
... Hi, I posted this question three weeks ago on BioStars, but now I'm posting it here too, hoping for some advice. I'm using DESeq2 to look for differentially expressed genes. I have three groups with different individuals: Treatment A, Treatment B, and Control. Sample sizes (individuals) differ bet ...
deseq deseq2 sample size written 6 weeks ago by glados0
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Comment: C: RNA-Seq data normalization/distribution problems [with pictures]
... No problem. Here it is.  What are you looking for in the plot? Trying to follow your thoughts. What do you expect it should look like? Green and red are from two different populations, so you think it's possible the difference is biological? ...
written 2.8 years ago by glados0
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Comment: C: RNA-Seq data normalization/distribution problems [with pictures]
... Thank you Michael for the suggestion. I have now edited the post and added the plot you requested and colSums. Plus a scatter plot of normalized counts. What do you think? ...
written 2.8 years ago by glados0

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