User: jjinhyoungkim

gravatar for jjinhyoungkim
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Canada
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3 years, 7 months ago
Joined:
3 years, 9 months ago
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Posts by jjinhyoungkim

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Group comparison in DESeq2
... Here is update what I did. I will try to run group comparison, if it is correct. Thanks again.   > coldata = data.frame(row.names = colnames(countMatrix),set = rep(c("gt1","gt2","gt3","gt4"),2,each = 2),condition = rep(c("control","treated"),each = 8)) > > coldata$condition = factor(x = c ...
written 3.7 years ago by jjinhyoungkim20
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Comment: C: Group comparison in DESeq2
... I tried to use the group comparison and got a error message as below. How can be it fixed? > coldata                     set condition Genotype1.1         gt1   control Genotype1.2         gt1   control Genotype2.1         gt2   control Genotype2.2         gt2   control Genotype3.1         gt3  ...
written 3.7 years ago by jjinhyoungkim20
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Comment: C: Group comparison in DESeq2
... Hi Michael Love, Great! Thanks for your help as always. ...
written 3.7 years ago by jjinhyoungkim20
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Group comparison in DESeq2
... Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions using the  two-way ANOVA design below. Referring a vignette of DESeq2, various comparisons have been run as below. Besides of these results, I want to get DEGs between groups (group1 vs each other group). Ho ...
deseq2 results written 3.7 years ago by jjinhyoungkim20 • updated 3.7 years ago by Michael Love23k
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All same padj of contrast results in the DESeq2
... Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions. In the comparison using "result ( contrast)", some comparisons had all same padj (0.9999874). Is it normal or anything wrong? FYI, the code are below. Thank you in advance for your time. >library("DESe ...
deseq2 contrast padj results written 3.7 years ago by jjinhyoungkim20 • updated 3.7 years ago by Michael Love23k
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Comment: C: DESeq2: Starting from count tables
... Thank you for your suggestion. I will do it as you recommended. ...
written 3.7 years ago by jjinhyoungkim20
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Comment: C: DESeq2: Starting from count tables
... Sorry again, I am in trouble with another error below. > library(DESeq2) > library("DESeq2") > countMatrix <- read.table ("~/Desktop/KiPBSvsPIC.txt", header=TRUE) > head (countMatrix)                ID Genotype1.1 Genotype1.2 Genotype2.1 Genotype2.2 Genotype3.1 1 unigene22398972      ...
written 3.7 years ago by jjinhyoungkim20
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Comment: C: DESeq2: Starting from count tables
... Thank you guy for your help. ...
written 3.7 years ago by jjinhyoungkim20
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DESeq2: Starting from count tables
... Hello, I am a novice for R and bioinfomatics. I am trying to run DESeq2 with my raw count table. I have been trying to follow the beginner's guide for the DESeq2 package, but it is still hard to understand because my experimental condition is different from the example. I tried to run with a kind h ...
deseq2 written 3.7 years ago by jjinhyoungkim20 • updated 3.7 years ago by Michael Love23k

Latest awards to jjinhyoungkim

Popular Question 3.6 years ago, created a question with more than 1,000 views. For DESeq2: Starting from count tables
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Group comparison in DESeq2

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