User: Researcher

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Researcher70
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Posts by Researcher

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Are the deconvolved gene expression values (already in fraction) from Cibersotx normalized or require any further normalization like TMM?
... 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 ...
cibersortx deconvolution gene expression written 10 weeks ago by Researcher70
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Comment: C: Integration of the TCGA's Agilent 244K and Affymetrix data
... 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 Researcher70
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Integration of the TCGA's Agilent 244K and Affymetrix data
... 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 ...
gene expression agilent 244k tcga affymetrix written 3 months ago by Researcher70 • updated 3 months ago by jared.andrews078.6k
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Comment: C: Using limma to find differentially methylated probes across clusters
... 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 Researcher70
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Comment: C: How to identify cluster membership from the tSNE coordinates?
... 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 Researcher70 • updated 6 months ago by GenoMax96k
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How to identify cluster membership from the tSNE coordinates?
... How to extract or identify cluster membership for each sample using the tSNE coordinates generated from rtsne? Its really urgent, kindly help. Thanks ...
tsne dimention reduction dimensionality reduction written 6 months ago by Researcher70 • updated 6 months ago by Mensur Dlakic9.0k
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Comment: C: How does AverageExpression() and aggregateData() differ from each other?
... That's true. I'll write to them. Thanks! ...
written 6 months ago by Researcher70
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Comment: C: How does AverageExpression() and aggregateData()
... 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 Researcher70
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Comment: C: Problem with AverageExpression() in Seurat
... Sure,Thanks for your help. ...
written 6 months ago by Researcher70
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How does AverageExpression() and aggregateData() differ from each other?
... 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. ...
averageexpression suerat aggregatedata written 6 months ago by Researcher70

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