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User: hamza_karakurt

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Posts by hamza_karakurt

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Hello Aaron, Thank you for your answer. You are right I am little confused. BuildSNNGraph uses Euclidean distance but the SNN matrix is a similarity matrix I believe (that's why silhouetteplots with that matrix does not work and you added warning to tutorial "We do not use the silhouette coefficient ...
written 1 day ago by hamza_karakurt0
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Comment: C: Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Thank you Aaron, This function is looking so useful. I believe the SNN matrix is a similarity matrix. I tried silhouette plots before but the results were always so bad (-1). Now I see the reason. I just have a small question. Does buildSNNGraph uses Euclidean distance or Jaccard index as a measure ...
written 5 days ago by hamza_karakurt0
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Silhouette Plots for Clustering Quality (Multiple Algorithm)
... Hello everyone, I am working on a scRNA-Seq data with multiple clustering algorithms. I want to see the quality of clustering with Silhouette plot function of "cluster" package. As I know, the function requires a distance matrix. Now my data is stored in Seurat object (can be transformed to SingleCe ...
clustering rna-seq scrna-seq silhouette plot written 15 days ago by hamza_karakurt0 • updated 14 days ago by Aaron Lun22k
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Deconvolution Method in Seurat and convert from SingleCellExperiment
... Hello everyone, I am working on scRNA-Seq data analysis. I mainly focused on Scater and Seurat. For some visual properties I (and my PI) want to use Seurat too but it only has LogNormalization. I believe it just takes the logarithm (in Seurat it is natural log not log2 I think). I want to use decon ...
rnaseq scater seurat singlecellexperiment written 9 weeks ago by hamza_karakurt0 • updated 8 weeks ago by Gordon Smyth36k
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Comment: C: Seurat to SingleCellExperiment Converting error in MAC
... Thank you so much. It worked. ...
written 3 months ago by hamza_karakurt0
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Seurat to SingleCellExperiment Converting error in MAC
... Hello everyone, I just started to work with MAC and using my own computer (Windows) as a tester. I am trying to convert a Seurat object to SingleCellExperiment with Convert function of Seurat package. It works in Windows but does not work in MAC. Also, is there a way in Scater package to read 10X ...
rnaseq single-cell singlecellexperiment written 3 months ago by hamza_karakurt0 • updated 3 months ago by Steve Lianoglou12k
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Comment: C: newSCESet and SingleCellExperiment basic differences and TMM Normalization
... Hey Aaron, Thank you for your answer. I will use calcNormFactors in scater. After this line, I need to multiply my SumFactors with my counts to normalize right? Or after computeSumFactors, directly normalize(sce) command does not do the job? I am working on unique barcoded single cell RNA-Seq.   ...
written 4 months ago by hamza_karakurt0
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newSCESet and SingleCellExperiment basic differences and TMM Normalization
... Hello everyone, I am trying to replicate a single cell RNA-Seq data analysis. Actually, the main problem is version. The old results were generated via newSCESet and normalized with normaliseExprs command (TMM method) but for the newest version of R, Bioconductor and packages so I used SingleCellEx ...

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