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Update 08b_time_course_analyses.md
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hwick authored May 10, 2024
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Expand Up @@ -41,7 +41,7 @@ dds <- DESeqDataSetFromMatrix(countData = raw_counts, colData = metadata, design

dds_lrt_time <- DESeq(dds, test="LRT", reduced = ~ genotype + treatment + time)
```
To understand what kind of gene expression patterns will be identified as differentially expressed, we have a few examples below. In the plots below we have gene expression on the x-axis and Time on the y-axis. In this dataset there are two samples for each time point, one having undergone some treatment (red) and the other without (blue).
To understand what kind of gene expression patterns will be identified as differentially expressed, we have a few examples below. In the plots below we have Time on the x-axis and gene expression on the y-axis. In this dataset there are two samples for each time point, one having undergone some treatment (red) and the other without (blue).

For this figure, we are depicting the type of **genes that will not be identified as differentially expressed.** Here, we observe that GeneX is differentially expressed between the time points, however there is no difference in that expression pattern between the treatment groups.

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