User: Researcher
Researcher • 70
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Posts by Researcher
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... Hi all, i am using Cibersotx to deconvolve TCGA gene expression data and getting my the expression values in fractions. I am not sure whether these should be considered as normalized count to perform differential expression among samples or we require any normalization as TMM in EdgeR. Anybody has a ...
written 10 weeks ago by
Researcher • 70
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... Hi @[jared][1],
Thank you for your kind reply.
My question is more about the gene expression, where they share 10779 genes for TCGA-GBM. Would it be recommended to use the expression values from the two in a common matrix and do some batch correction?
Thanks
[1]: https://www.biostars.org/u/401 ...
written 3 months ago by
Researcher • 70
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... Hello All,
Can we integrate the Agilent 244K and Affymetrix data from TCGA?
Does anyone has some experience with this and can share any workflow, if there is any?
Thanks ...
written 3 months ago by
Researcher • 70
• updated
3 months ago by
jared.andrews07 ♦ 8.6k
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... Hi @[yura.grabovska][1] any update about your problem? I am interested to use the similar approach, kindly help.
[1]: https://www.biostars.org/u/39702/ ...
written 4 months ago by
Researcher • 70
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... Hi, Sorry for the incomplete question I asked.
Actually, its a two-dimensional reduction of TCGA methylation data. I have used Rtsne() as given below and identified three different clusters of three main groups in the data.
> tsne_realData <- Rtsne(meth, perplexity=30, max_iter=500,learni ...
written 6 months ago by
Researcher • 70
• updated
6 months ago by
GenoMax ♦ 96k
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... How to extract or identify cluster membership for each sample using the tSNE coordinates generated from rtsne?
Its really urgent, kindly help.
Thanks ...
written 6 months ago by
Researcher • 70
• updated
6 months ago by
Mensur Dlakic • 9.0k
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... That's true. I'll write to them. Thanks! ...
written 6 months ago by
Researcher • 70
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... Hi [Kevin][1],
Thanks for sharing these links here. Actually I didn't ask my question clearly.
My doubt is **Seurat's AverageExpression() should exactly be the same as muscat's aggregateData() with fun="mean"**.
As both are just the average gene expression values from a group of cells from each of ...
written 6 months ago by
Researcher • 70
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... Sure,Thanks for your help. ...
written 6 months ago by
Researcher • 70
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... Can someone please explain how does Seurat's AverageExpression() differ from muscat's aggregateData() and which one is better to get average expression of genes for each cluster?
Thanks in advance. ...
written 6 months ago by
Researcher • 70
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