User: sharmila.ahmad

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Posts by sharmila.ahmad

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Summary results interpretation in DeSeq2
... 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 8 weeks ago by sharmila.ahmad0
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Comment: C: Summary results interpretation in DeSeq2
... Thank you for your explanation. Best, Mila ...
written 9 weeks ago by sharmila.ahmad0
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Summary results interpretation in DeSeq2
... 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 ...
deseq2 written 9 weeks ago by sharmila.ahmad0 • updated 9 weeks ago by Michael Love23k
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Comment: C: Error in checkFullRank(modelMatrix) :
... 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 10 weeks ago by sharmila.ahmad0
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Error in checkFullRank(modelMatrix) :
... 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 ...
deseq2 written 10 weeks ago by sharmila.ahmad0 • updated 10 weeks ago by Michael Love23k
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Comment: A: How to create 3 way interactions model for Deseq
... 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 10 weeks ago by sharmila.ahmad0
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How to create 3 way interactions model for Deseq
... 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 ...
deseq2 written 10 weeks ago by sharmila.ahmad0

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