User: jdhindsa1999
jdhindsa1999 • 0
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Posts by jdhindsa1999
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C: DESeq multiple factor question
... Thank you very much for the help! I've manually edited my matrix and then provided it to DESeq. I reordered my genotypes using `ddsHTSeq_filtered$Genotype <- factor(ddsHTSeq_filtered$Genotype, levels = c("WT", "mdx", "d52"))`
Now my question remains in extracting the relevant contrasts, as you ...
written 8 days ago by
jdhindsa1999 • 0
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C: DESeq multiple factor question
... Thank you all for the help! Do you have any suggestions on how to analyze the data given that I don't have d52 p8? Should I do the analysis separately for the p8 and then analyze the 6m and 12m together? ...
written 12 days ago by
jdhindsa1999 • 0
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C: DESeq multiple factor question
... Thank you for the help. However, when I try to include the interaction term, I get an error saying that the model matrix is not full rank. Do you know if this is an issue with the way the experiment was designed? I am attaching an image of my samples. [samples][1]
![enter image description here][2]
...
written 12 days ago by
jdhindsa1999 • 0
• updated
12 days ago by
GenoMax ♦ 96k
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... Hi,
This is my first time using the DESeq2 package for RNA-seq analysis. I am analyzing a longitudinal study of three different time points in mice, with three different genotypes of animals - 1 wildtype, 2 mutated. I want to evaluate differential expression as an effect of the different genotypes ...
written 12 days ago by
jdhindsa1999 • 0
• updated
12 days ago by
Carlo Yague ♦ 5.7k
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... Thanks so much for the help! Would the ls command be appropriate instead of the find command?
...
written 28 days ago by
jdhindsa1999 • 0
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... Hello,
I am new to RNA-seq analysis, and I am attempting to align my sequence reads to my indexed genome in STAR (I've already indexed the genome). I have 50 samples in total, and each sample has 4 respective fastq.gz files – this was PE with 50 bp reads, and run in two lanes. Thus, per sample, 2 ...
written 28 days ago by
jdhindsa1999 • 0
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