User: Researcher

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Researcher60
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Posts by Researcher

<prev • 83 results • page 1 of 9 • next >
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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 4 weeks ago by Researcher60 • updated 29 days ago by genomax89k
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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 4 weeks ago by Researcher60 • updated 4 weeks ago by Mensur Dlakic6.4k
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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 5 weeks ago by Researcher60
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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 5 weeks ago by Researcher60
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Comment: C: Problem with AverageExpression() in Seurat
... Sure,Thanks for your help. ...
written 5 weeks ago by Researcher60
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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 5 weeks ago by Researcher60
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Comment: C: Problem with AverageExpression() in Seurat
... @[Friederike][1], It is GetAssayData(test_sct)['EGFR',] %>% summary Min. 1st Qu. Median Mean 3rd Qu. Max. -13.4363 -1.7349 0.3935 1.5173 4.1848 21.8560 Note: This summary is from the whole dataset. But I want this for each of the cluster or cell type ...
written 5 weeks ago by Researcher60 • updated 5 weeks ago by genomax89k
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Comment: C: Problem with AverageExpression() in Seurat
... Hi [Friederike][1], Just to clarify, I have data from 9 different samples. These were first merged and this how the GetAssayData() looks like: GetAssayData(test)['EGFR',][1:5] STR_AAACCCACAGGCTTGC STR_AAACCCAGTCGTCTCT STR_AAACCCAGTGGAACCA STR_AAACCCATCAAGCCGC STR_AAACCCATCGTGGAAG ...
written 5 weeks ago by Researcher60 • updated 5 weeks ago by genomax89k
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Problem with AverageExpression() in Seurat
... Hi, I am trying to calculate the average expression using the given command: cluster.averages <- AverageExpression(test) and referring RNA values to export its raw counts but getting *"Inf"* as its value for most of the genes. Example: cluster.averages$RNA['EGFR','Tumor Cells'] [ ...
averageexpression scrna seq seurat clusters written 5 weeks ago by Researcher60 • updated 5 weeks ago by zx87549.6k
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How to convert 10X single nuclear RNA Seq bam file to fastq?
... Hi All, I have 10X single-nuclear RNA Seq bam files and want to convert these to fastq files. I am not sure how can we do this? Will this be similarly treated as we handle scRNA Seq bam files using bamtofastq? Thanks ...
bamtofastq 10x genomics cellranger snrna written 3 months ago by Researcher60

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