User: Emily

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Emily0
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Posts by Emily

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Comment: C: DESeq2 Model Design
... Thank you very much, Michael. Cheers! ...
written 4.3 years ago by Emily0
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Comment: C: DESeq2 Model Design
... Thanks Michael, So you mean that I do not need to change the full modle or reduced modle when I try to compare specific time points within a treatment or the treatment differences within a single time point, and the precedence order of the "Treatment" and "TimePoint" in the full or reduced modle wi ...
written 4.3 years ago by Emily0
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Comment: C: DESeq2 Model Design
... Hi Michael and Andrew, I have a question that I was puzzling. To look at differences between two different time points for a specific treatment, using the reduced model as: reduced=~Treatment + TimePoint. To look at the differences between Treatment A and Treatment B at a specific time point, does t ...
written 4.3 years ago by Emily0
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Answer: A: PCA analysis of the RNASeq data
... Hi Aaron, thanks for your reply. The dot in my description of the data means the value, I did not give the actual value for each datapoint, just use dot instead. The command I used to generate the PCA plot is as follows: library(psych) library(GPArotation) data = read.table("C:\\Users\\Desktop\\PC ...
written 4.4 years ago by Emily0
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gene expression analysis using fuzzy C-means by using Mfuzz package
... Hi everyone, I am analyzing the expression profile of about 12,000 genes, cluster analysis using  fuzzy C-means by using Mfuzz package in R. However, whether I use a C value of 100 or 50, for each cluster, I only got very few genes with a membership value higher than 0.7, say only 20 or 40 genes. T ...
rnaseq written 4.4 years ago by Emily0 • updated 4.4 years ago by b.nota340
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PCA analysis of the RNASeq data
... Hi everyone, I am doing a PCA analysis with my RNASeq data and I want to konw whether the genotypes have a great effect on the gene expression. I have four genotypes :G0(wild type),G1,G2,G3 and three time points: T1,T2,T3. All the values in the dataset are Log2FC values compared to wild type. The d ...
rnaseq R written 4.4 years ago by Emily0

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