User: Ahdee

gravatar for Ahdee
Ahdee40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
1 week, 1 day ago
Joined:
3 years, 7 months ago
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s********@gmail.com

Posts by Ahdee

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Why does limma voom E value give different result than the voom object
... @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 days 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 days ago by Ahdee40
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Why does limma voom E value give different result than the voom object
... 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" ...
limma voom rna-seq written 8 days ago by Ahdee40 • updated 8 days ago by thokall160
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Is there a package to convert DNA coordinates to Cytogenetic location?
... 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 ...
annotation coordinates cytogenetic written 7 weeks ago by Ahdee40
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Help with mapping Kegg hsa01100 using pathview
... 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 ...
pathview kegg pathway written 11 weeks ago by Ahdee40
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benefits of pearson distance for hierarchical clustering
... 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 ...
heatmap heatmap.3 written 5 months ago by Ahdee40 • updated 5 months ago by James W. MacDonald50k
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(Closed) Help with Censoring using the survival package.
... 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 ...
survival kaplan-meier survival analysis hazard ratio written 9 months ago by Ahdee40
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Comment: C: Where to download expected counts instead of normalized RSEM for TCGA LUAD?
... Steve, thanks, this is perfect.  the recount2 project looks awesome.  On top of that there is a R packages to make the download easier.  Found a great tutorial here in case anyone else is interested.  https://www.bioconductor.org/packages/devel/workflows/vignettes/recountWorkflow/inst/doc/recount-w ...
written 9 months ago by Ahdee40
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Where to download expected counts instead of normalized RSEM for TCGA LUAD?
... Dear all, this is not a typical R question but I'm wondering if anyone knows a url or even a package that can download expected_counts for the TCGA data like LUAD.  I can easily download the rsem gene normalize dataset from places like firehose however I need to run a DGE using something like edgeR ...
limma tcga written 9 months ago by Ahdee40 • updated 9 months ago by Steve Lianoglou12k
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Comment: C: Combining groups in a LIMMA design
... Great thank you for helping confirm this.  and yes I can now see that dividing by 2 is necessary. There is a strange issue however that, only on certain datasets,  for some weird reason, running all the groups together and than building the contrast, for example, in the  a = adult.control - adult.au ...
written 10 months ago by Ahdee40

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