User: hkarakurt
hkarakurt • 80
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Posts by hkarakurt
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... Thank you so much for your answer. I tried your advice but there is a problem apparently.
When I use "design = model.matrix( ~ 0 + exp )" about 95% of the genes are signficantly changed and it looks wrong.
With my codes it was about 30%.
What is the disadvantage of using "~exp" instead of "~0 + ex ...
written 4 weeks ago by
hkarakurt • 80
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... Hello,
I have a microarray gene expression data set consists 30 samples for two groups (Wild Type and Mutant) with certain time points. I want to do differential expression analysis between conditions but I want my analyses to consider time points too. My data looks like this:
Sample Condition Time ...
written 5 weeks ago by
hkarakurt • 80
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... They are completely different data sets from same biological sample ...
written 7 weeks ago by
hkarakurt • 80
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... I am planning to check tximport package to convert FPKM and TPM values to counts. I found the function. I think you mean that one. ...
written 7 weeks ago by
hkarakurt • 80
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... Thank you for your answer. My problem here is I do not have any raw count data. I am using public data sets and they provided only FPKM/TPM values.
I was using MNN before but I have never been in a situation like this (data with only FPKM data) ...
written 7 weeks ago by
hkarakurt • 80
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... Hello,
We are trying to analyze a set of single cell data sets from different sources but we have a problem. One of the data set is in TPM and another one is in FPKM format. It is easy to do batch correction with raw counts (with CCA in Seurat or MNN in Scater) but we have no idea how to deal with t ...
written 7 weeks ago by
hkarakurt • 80
• updated
7 weeks ago by
shoujun.gu • 250
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... Hello,
I have an interaction network with 18 nodes and 15000 edges. I want to visualize them in Cytoscape and give colors for each node automatically. I tried passthrough mapping but colors did not change at all. I know I can give color to each node manually but is there a way to do it easier?
Than ...
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... Thank you for your answer.
1) In fact, experiments were done in the single run in 10X but of course samples come from different mice as unpaired samples. When I tested the batch effect I saw there is little batch effect. I also tried MNN before.
The point is, if I do batch correction, I will lose t ...
written 4 months ago by
hkarakurt • 80
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... Thank you for your answer. As you mentioned, there are many possible methods to use. I prefer to do it in R/Bioconductor (it is not only my choice). I will check destiny and slingshot.
Thank you again. ...
written 4 months ago by
hkarakurt • 80
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3.3k
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... Thank you for you answer. Actually I used deconvolution method of Scran for normalization and used it as normalized data in Seurat.
With a small thinking, using that normalized values is not okay in my opinion because this methods does pooling across the cells and if I extract small proportion of ce ...
written 4 months ago by
hkarakurt • 80
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