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... Hi Michael, I have another few questions to ask; 1) regarding filtering the low gene counts and outliers using NOISeq before running the DESeq. It is necessary or recommended to do that? If yes, does it makes any difference since the DESeq itself will filter the outliers and low counts genes righ ...
written 4 months ago by sharmila.ahmad0
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... Thank you for your explanation. Best, Mila ...
written 4 months ago by sharmila.ahmad0
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... Hi and good day, Can anyone explain to me what should I do if got the following results after running DeSeq? What should I do with the outliers and low counts? I have had filtered the low count <5 before running the analysis. ### result for Sex (F as reference level) res_Sex <-result ...
written 4 months ago by sharmila.ahmad0 • updated 4 months ago by Michael Love24k
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... Thank you again for your reply. I completely agree with you that I should design the model based on the specific biological approach. What I did for now is combining the two factors (Ewed & Lambd) as a group and used it in the design = ~ group + Sex ...
written 4 months ago by sharmila.ahmad0
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... Hi, I am currently trying to run a deferential gene expression analysis to determine the the impact of Ewed (maternal diet) , Lambd (offspring diet) and sex (gender) on the mRNA expression of perirenal fat (per). My experimental design, therefore is three way interactions (Ewed: Lambd: Sex) and I wo ...
written 4 months ago by sharmila.ahmad0 • updated 4 months ago by Michael Love24k
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... Hi Micheal, Thank you for your feedback. I have tried to consult with someone that have knowledge in this matter but could not find any solution to that (for now) I have also tried to run this following model matrix but got error design <- model.matrix(~ -1 + per$Lambbw6 + per$Birthw + per\$L ...
written 4 months ago by sharmila.ahmad0
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... Hi good day, This is my first time working on differential gene expression analysis using DeSeq2. I am having a problem to construct my model matrix for DeSeq2 since I have a very complex experimental design (3 factors design) with the following information; ID Ewed Lambd Sex 1768 HIGH CONV M 1774 ...
written 4 months ago by sharmila.ahmad0