User: ucheuna

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ucheuna0
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Posts by ucheuna

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Multiple pairwise comparisons
... I have a dataset with 4 time points: 3months, 6months, 1year, 2years and two conditions within each timepoint: WT and KO. I wish to find diff expressed genes between WT and KO from 3months to 6 months, 6 months to 1year, 1year to 2years, 3months to 2years, 3months to 1year, 6months to 2years. I used ...
design and contrast matrix written 2.2 years ago by ucheuna0
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ggplots gives errors
... Hey Mike, while following the time course experiments vignette, I continue to get an error when I use the code below: fiss <- plotCounts(ddsTC, which.min(resTC$padj), intgroup = c("minute","strain"), returnData = TRUE) ggplot(fiss, aes(x = as.numeric(minute), y = count, ...
rnaseq ggplot2 written 2.2 years ago by ucheuna0 • updated 2.2 years ago by Matthias Z.20
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Comment: A: DESeq2 for multiple comparisons over time
... Also even after reading the excerpt, my initial question still stands regarding the results:  [1] "Intercept"          "Age_2YR_vs_1YR"     "Age_3M_vs_1YR"      "Age_6M_vs_1YR"      [5] "condition_WT_vs_KO" "Age2YR.conditionWT" "Age3M.conditionWT"  "Age6M.conditionWT"  ...
written 2.2 years ago by ucheuna0
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Comment: A: DESeq2 for multiple comparisons over time
... Hey Mike, I have performed LRT using the following three sets of codes exempting time and even genotype:  > dds <- DESeq(dds, test = "LRT", reduced = ~ Age + condition) > dds <- DESeq(dds, test = "LRT", reduced = ~ Age)  > dds <- DESeq(dds, test = "LRT", reduced = ~ condition) ...
written 2.2 years ago by ucheuna0
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Comment: A: DESeq2 for multiple comparisons over time
... Hey Mike, After running the first chunk of code in the Time course experiments chapter, here are results I received: [1] "Intercept"          "Age_2YR_vs_1YR"     "Age_3M_vs_1YR"      "Age_6M_vs_1YR"      [5] "condition_WT_vs_KO" "Age2YR.conditionWT" "Age3M.conditionWT"  "Age6M.conditionWT"  >  ...
written 2.2 years ago by ucheuna0
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Comment: A: DESeq2 for multiple comparisons over time
... Thanks Mike for the quick response, I am interested in performing both pairwise comparisons and significant genes at each timepoint between knockout and wild type ...
written 2.2 years ago by ucheuna0
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DESeq2 for multiple comparisons over time
... I wish to know genes that are significantly expressed between knockout and wild type mice as they age from 3 months, 6 months, 12months and 24months. I wonder the best way to analyze such data. I combined Age and condition (genotype) and performed DESeq2 as follows:  > coldata$Age_condition < ...
deseq multiple factor design written 2.2 years ago by ucheuna0

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 for multiple comparisons over time

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