User: hkarakurt

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hkarakurt80
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Posts by hkarakurt

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Differential Expression Analysis of Two Groups Time Series Data with Limma
... 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 hkarakurt80
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Differential Expression Analysis of Two Groups Time Series Data with Limma
... 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 ...
microarray limma rna-seq differential expression written 5 weeks ago by hkarakurt80
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Comment: C: Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... They are completely different data sets from same biological sample ...
written 7 weeks ago by hkarakurt80
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Comment: C: Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... 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 hkarakurt80
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Comment: C: Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... 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 hkarakurt80
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Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
... 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 ...
scrna-seq batch correction fpkm tpm rna-seq written 7 weeks ago by hkarakurt80 • updated 7 weeks ago by shoujun.gu250
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Automatic Coloring for Each Node According to Names in Cytoscape
... 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 ...
network intercation cytoscape written 4 months ago by hkarakurt80 • updated 4 months ago by scooter110
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Comment: C: Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
... 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 hkarakurt80
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Comment: C: Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
... 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 hkarakurt80
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Comment: C: Using Seurat 3 Data for Pseudotime Analysis in Monocle 3
... 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 hkarakurt80

Latest awards to hkarakurt

Supporter 7 weeks ago, voted at least 25 times.
Popular Question 4 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 4 months ago, created a question with more than 1,000 views. For How to extract expression data from RAW data.
Popular Question 4 months ago, created a question with more than 1,000 views. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 4 months ago, created a question with more than 1,000 views. For Differential Coexpression Analysis
Student 4 months ago, asked a question with at least 3 up-votes. For Mitochondrial Gene percentage threshold in single cell RNA-Seq
Popular Question 7 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 8 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 13 months ago, created a question with more than 1,000 views. For Tool for predicting transcription factors from a gene list
Popular Question 17 months ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis
Popular Question 19 months ago, created a question with more than 1,000 views. For Retrieving data from NCBI GEO and RNA-Seq Data Analysis

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