User: Ahdee

gravatar for Ahdee
Ahdee40
Reputation:
40
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New User
Location:
United States
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1 week, 2 days ago
Joined:
3 years, 5 months ago
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Posts by Ahdee

<prev • 31 results • page 1 of 4 • next >
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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 14 days 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 3 months ago by Ahdee40 • updated 3 months ago by James W. MacDonald49k
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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 7 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 7 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 7 months ago by Ahdee40 • updated 7 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 7 months ago by Ahdee40
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Combining groups in a LIMMA design
... Hi all I have a design that I'm wondering if someone can help me double check.  Basically I have he following groups.  Adult.autism  Peds.autism Adult.control Peds.control  I want to do the following comparisons * compare ped control vs. ped autism  * compare adult control vs adult autism * ped a ...
limma written 7 months ago by Ahdee40
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Comment: C: Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
... Gordon, ok thanks. I will just do the the analysis separately on certain subsets.  A.  ...
written 8 months ago by Ahdee40
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Run edgeR or Voom+LIMMA where groups are dynamically reassigned for each gene.
... HI, this is a bit of odd request.  But is it possible to reassign or combine groups?    For example say I have  simple group like this:  group <- c( "a" ,"a", "a" ,"b", "b", "b" ) design <- model.matrix(~0+ factor ( group ) ) fit  <- lmFit( data , design ) contrast.matrix <- makeContra ...
rnaseq limma edger written 8 months ago by Ahdee40 • updated 8 months ago by Gordon Smyth36k
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Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
... Dear all, I have a dataframe consisting of tpm count generated from another group using RSEM.  However, this only comes with tpm counts only. My goal is to use tximport to convert to this to a count-matrix to use with something like voom-limmar, however the the tutorial I can find so far gives a exa ...
limma rna-seq tximport written 16 months ago by Ahdee40 • updated 16 months ago by Michael Love22k

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