User: f.morgana
f.morgana • 0
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Posts by f.morgana
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... 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.morgana • 0
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... 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 ...
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... 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 ...
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... 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.morgana • 0
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... 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.morgana • 0
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... 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 . ...
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... 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 ...
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... @ genomax: Thanks so much genomax, you have been so helpful, I will give this a try! ...
written 10 months ago by
f.morgana • 0
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... 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.morgana • 0
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... 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 ...
written 10 months ago by
f.morgana • 0
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