User: f.morgana

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f.morgana0
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Posts by f.morgana

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Error in function heatmap: 'x' must be a numeric matrix
... Hi JC, Many thanks for your rapid response! I tried your suggestion, it seems to fix my previous error but now I get another one stating: Error in heatmap(as.matrix(log1p(heatdata)), Colv = NA, ColSideColors = brewer.pal(9, : 'ColSideColors' must be a character vector of length ncol(x ...
written 5 months ago by f.morgana0
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Error in function heatmap: 'x' must be a numeric matrix
... Hi all, I have been struggling with the heatmap function for which I continuously receive the error: 'x' must be a numeric matrix. I have been trying to perform section 4 ("Identifying temporally expressed genes") of the following slingshot vignette: http://www.bioconductor.org/packages/devel/bioc ...
slingshot tradeseq heatmap written 5 months ago by f.morgana0 • updated 3 months ago by Biostar ♦♦ 20
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Difference between "LogNormalize" normalization method in Seurat and z score normalization
... Hi all, Perhaps a silly question but the default normalization method in Seurat is "LogNormalize". Instead of automatically running the code, I would like to understand what is happening when I perform the normalization and scaling steps in Seurat. And how exactly does this differ from z score nor ...
normalization z-score seurat scrnaseq statistics written 8 months ago by f.morgana0 • updated 8 months ago by ATpoint44k
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Comment: A: How to remove entire rows from seurat object based on cellhash read
... Hi there, I tried to remove certain rows in my dataset as well using this function. Sample donor organ sort method file is.TRA.p is.TRB.p is.TRA.np FCAImmP7179369-AAACGGGTCTGTCAAG 6 3 0 1 0 2 FALSE FALSE FALSE FCAIm ...
written 8 months ago by f.morgana0
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Comment: C: CellScatter function Seurat not working
... Thank you for the link to the guideline for images, geek_y! I indeed could distinguish clear clusters to my opinion (although I only had a little more than 300 cells). Here's my attempt to posting images then: ![this is what my tSNE looks like][1] ![this is what the cell scatter plot looks l ...
written 8 months ago by f.morgana0
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Comment: C: CellScatter function Seurat not working
... Hi geek_y, Of course: > head(cluster.averages[["RNA"]][, 1:3]) 6 x 3 sparse Matrix of class "dgCMatrix" 1 2 3 A1BG 0.14812722 0.178343100 0.12386361 A1CF 0.02273091 0.006427456 0.06277195 A2M-AS1 0.02273091 0.073081493 . ...
written 9 months ago by f.morgana0 • updated 9 months ago by geek_y11k
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CellScatter function Seurat not working
... Hi all, I am trying to plot the average gene expression of two clusters within my single cell RNAseq data using the CellScatter function (Seurat). I followed the exact steps of the vignette, however my plot looks like a black square sheet of evenly distributed cells instead of a proper cell scatte ...
scrna-seq cellscatter seurat written 9 months ago by f.morgana0 • updated 9 months ago by ATpoint44k
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Comment: A: Downloading FASTQ files from ArrayExpress very slow
... @ genomax: Thanks so much genomax, you have been so helpful, I will give this a try! ...
written 10 months ago by f.morgana0
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Comment: A: Downloading FASTQ files from ArrayExpress very slow
... Thanks for your rapid responses genomax and ATpoint! @ genomax many thanks for your suggestion, here is the concerned accession number: E-MTAB-8581. I think I managed to find the files now on NCBI but I cannot find where to download the actual FASTQ files. Do you have any idea how I could retrieve ...
written 10 months ago by f.morgana0
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Downloading FASTQ files from ArrayExpress very slow
... Hi all, I am trying to download FASTQ files from ArrayExpress from a particular publication but it is going at an extremely slow rate. I started with attempting to download one FASTQ file of 3.85 GB. After a while I get the notification that it failed to download. Is this a known problem? How I ...
arrayexpress fastq scrnaseq sequencing written 10 months ago by f.morgana0

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