User: Researcher
Researcher • 60
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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 4 weeks ago by
Researcher • 60
• updated
29 days ago by
genomax ♦ 89k
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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 4 weeks ago by
Researcher • 60
• updated
4 weeks ago by
Mensur Dlakic • 6.4k
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... That's true. I'll write to them. Thanks! ...
written 5 weeks ago by
Researcher • 60
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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 5 weeks ago by
Researcher • 60
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... Sure,Thanks for your help. ...
written 5 weeks ago by
Researcher • 60
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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 5 weeks ago by
Researcher • 60
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... @[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
Researcher • 60
• updated
5 weeks ago by
genomax ♦ 89k
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... 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
Researcher • 60
• updated
5 weeks ago by
genomax ♦ 89k
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... 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']
[ ...
written 5 weeks ago by
Researcher • 60
• updated
5 weeks ago by
zx8754 ♦ 9.6k
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... 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 ...
written 3 months ago by
Researcher • 60
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