User: dz2353

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dz235350
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2 months, 2 weeks ago
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d*****@columbia.edu

Posts by dz2353

<prev • 11 results • page 1 of 2 • next >
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Answer: A: FPKM and DESEq - RNAseq
... Hi, As swbarnes said, you need to use reads count matrix as an input file. Before you use DESeq2 to analyze your data, you need to do some filter work in order to delete low expressed genes. After doing DESeq analysis, you will get a normalized gene expression matrix, and then you will do PCA analy ...
written 9 weeks ago by dz235350
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Comment: C: How to use the data from SRA database?
... Thanks for your detailed reply. I think I made a mistake. My case is that I have three amniotic epithelial cell samples (AECs), and I want to find out the differently expressed genes between AECs and hESC. Obviously, the relationship between AEC and hESC is not that as I mentioned before. I download ...
written 10 weeks ago by dz235350
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Comment: C: How to use the data from SRA database?
... Maybe I need to make it more clear. My case is that I have three amniotic epithelial cell samples (AECs), and I want to find out the differently expressed genes between AECs and hESC. However, I do not have hESC's data, so I have to download some from the SRA database. Actually, I did find some hESC ...
written 10 weeks ago by dz235350
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How to use the data from SRA database?
... Dear friends, Maybe the post title is not described accurately, but I do not know how to say it. I want to download some data from SRA database on NCBI as a control group to make a comparison with my treatment group so that I can do some downstream analysis like differently expressed genes analysis. ...
next-gen rna-seq written 10 weeks ago by dz235350 • updated 10 weeks ago by WouterDeCoster36k
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Wow, much clear and so appreciate it! ...
written 10 weeks ago by dz235350
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Answer: A: Pathway analysis and Gene enrichment Analysis Queries
... Hi, Maybe you can try this one: Metascape (web-based). For pathway analysis, I used IPA but is a commercial software. ...
written 10 weeks ago by dz235350
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Well, thanks for your answer, Kristoffer. So what you mean is that I use gene id instead of gene name or symbols? But I still have some points unclear. You mentioned that you always analyze the data with gene ids (here is the Ensembl ID ), so what kind of analysis you do? I want to perform a PCA ana ...
written 10 weeks ago by dz235350
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Thank you! I will try it. ...
written 11 weeks ago by dz235350
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... I know that the part after decimal point represents the version. So what I need to do is to delete the parts after .decimal point and then transfer the Ensembl id to gene symbol? Thanks in advance for the reply! ...
written 11 weeks ago by dz235350
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Sorry, I made a mistake. Thanks for @arup's comment. I correct my question as an Ensembl id matches multiple gene symbols. And I post a pic for my data and you can see that there are so many RF00019. Should I add all of them together? ! https://ibb.co/9T1xkBD ...
written 11 weeks ago by dz235350

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