## User: Ahdee

Ahdee40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
2 weeks, 2 days ago
Joined:
3 years, 9 months ago
Email:
s********@gmail.com

#### Posts by Ahdee

<prev • 38 results • page 1 of 4 • next >
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... Thanks James and Gordon! This is very reassuring - I been using single models ( that is analyzing everything together and using contrast to parse out the different comparison ) however started to freak out mostly because the logfc were different. I though that logFC was simply calculated from the j ...
written 6 weeks ago by Ahdee40
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... Thanks James, I should be more specific. This is for an RNA-seq that has been TMM normalized and voom. I'm using voom as the input. So in general what you are saying is that leaving everything as a single model and defining the contrast is "better" but only if the variance between the samples are n ...
written 6 weeks ago by Ahdee40
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... Hi suppose I have these 3 groups, a b and c. data= c ( rep("a", 3), rep("b",3), rep("c",3) ) mm = model.matrix(~0 + data ) colnames( mm ) = c("a","b","c") makeContrasts( avsb = a - b, levels=mm) a b c 1 1 0 0 2 1 0 0 3 1 0 0 4 0 1 0 5 0 1 0 ...
written 6 weeks ago by Ahdee40 • updated 6 weeks ago by James W. MacDonald50k
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... @thokall oh yes that right. I read it more carefully now whereby I thought previously that the E value were not only normalized but weighted as well, my bad, thanks! ...
written 8 weeks ago by Ahdee40
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Comment: C: Seurat 2.3.4 installation
... Hi you could also install directly from github. However first you need to remove.packages("Seurat") then make sure that you have install.packages("devtools") library(devtools); devtools::install_github(repo = 'satijalab/seurat', ref = 'release/2.4', dependencies=T) make sure to rest ...
written 8 weeks ago by Ahdee40
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... Hi so I notice something interesting. data <- voom(x, plot=T, design = design2) vfit <- lmFit(data) vfit <- eBayes(vfit) topTable(vfit,coef=2,sort.by="P") vfit <- lmFit(data\$E, design = design2) vfit <- eBayes(vfit) topTable(vfit,coef=2,sort.by="P" ...
written 9 weeks ago by Ahdee40 • updated 8 weeks ago by thokall160
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... Hi I was wondering if there is package to draw chromosome and/or list out cytogenetic locations based on DNA location. For example here is hg19, chr15:69,373,210-69,373,239. thanks! A ...
written 3 months ago by Ahdee40
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... Dear all, recently I did an enrichment analysis showing that my RNA.seq data is enriched for the global pathway hsa01100, however on trying to plot this with pathview it does not seem to highlight the genes. I found a similar post previously but its not exactly what I wanted since I'm interested i ...
written 4 months ago by Ahdee40
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... Dear all, I notice recently that  the heatmap3 package uses pearson distance instead of the default euclidean/manhattan. as.dist(1 - cor(df, use = "pa"))   Is there a benefit of using correlation instead of euclidean when it comes to calculating distance? The reason why I ask is because the hea ...
written 7 months ago by Ahdee40 • updated 7 months ago by James W. MacDonald50k
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... Hi all I would like to do some survival analysis using the survival package. The most difficult part for me is setting up the censoring data correctly and I would appreciated if someone can help confirm if I'm doing this correctly. According to the ?Surv function. "For interval censored data, the s ...
written 11 months ago by Ahdee40

#### Latest awards to Ahdee

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