User: CandiceChuDVM

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CandiceChuDVM1.3k
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United States/College Station/Texas A&M University
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Posts by CandiceChuDVM

<prev • 55 results • page 1 of 6 • next >
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Comment: C: How to perform edgeR based on serial paired samples?
... Hi Devon, When I apply `design <- model.matrix(~0 + subject + group)`, the `colnames(design)` are: [1] "subject1" "subject2" "subject3" "subject4" [5] "groupaffected_t2" "groupaffected_t3" "groupcontrol_t1" "groupcontrol_t2" [9] "groupcontrol_t3" ...
written 3 months ago by CandiceChuDVM1.3k
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How to perform edgeR based on serial paired samples? (model.matrix design)
... Hi all, I have 4 paired samples in treatment vs control at 3 different time points. How can I set up a `model.matrix` so I can treat them as paired samples and compare the following comparisons in `glmLRT` of edgeR: 1. Treatment vs control (paired samples), regardless of time 2. Treatment vs ...
R edger rna-seq written 3 months ago by CandiceChuDVM1.3k
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Answer: A: Small RNA-seq experimental design, pooling samples or not ? which one is better?
... Thanks for all replies. I think we have reached a conclusion that pooling isolated RNA is preferred over pooling biofluids. For the question "to pool or not to pool", the aforementioned papers only provide limited information. I've found another paper "[Experimental validation of methods for diff ...
written 5 months ago by CandiceChuDVM1.3k
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Comment: C: Small RNA-seq experimental design, which one is better?
... I understand your point. No doubt we should have as many biological replications as we can (I can have up to 10 per disease). Since you mentioned "without pooling", I was wondering how sample pooling would affect the statistical power if the numbers of lib. prep. are the same? Any reference? ...
written 5 months ago by CandiceChuDVM1.3k
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Small RNA-seq experimental design, pooling samples or not ? which one is better?
... Hi all, I have 3 types of diseases and one control group. Each disease has 10 samples. Ideally we would like to have individual library preparations (lib. prep.) for each sample, however, our budget won't be able to afford it. So that leaves us with one option: pooling samples. For sample pooling ...
pooling small rna-seq mirna-seq microrna rna-seq written 5 months ago by CandiceChuDVM1.3k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Thanks! I wasn't aware of that. I will contact SRA later to figure out what to do at this point. ...
written 6 months ago by CandiceChuDVM1.3k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Yes. I have tried ftp using the following instruction: > After you login, > 1. navigate to your account folder: cd uploads/candicechu@tamu.edu_TsOpWGZR > 2. create a subfolder with a meaningful name (required): mkdir new_folder > 3. navigate to that folder: cd new_folder > 4. ...
written 6 months ago by CandiceChuDVM1.3k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... I can't agree more with you. ...
written 6 months ago by CandiceChuDVM1.3k
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Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Hi all, I am writing this tutorial in response to my previous question: [NCBI SRA submission: neither sample_name nor biosample_accession are set][1]. I took me three days to figure our what's going on so I hope my tutorial can save your time and make your life easier: [Tutorial: How to upload y ...
ncbi sra tutorial biosample bioproject written 6 months ago by CandiceChuDVM1.3k • updated 9 weeks ago by Lucila10
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NCBI SRA submission: neither sample_name nor biosample_accession are set
... Hi all, I am not sure if this question still belongs to the scope of BioStars. It is my first time submitting mRNA-Seq data to SRA for publication so I wish somebody who has experience can shed some lights on my problem. Since I have no previous submission whatsoever. I am trying to complete both ...
ncbi sra sequence read archive rna-seq written 6 months ago by CandiceChuDVM1.3k

Latest awards to CandiceChuDVM

Appreciated 9 weeks ago, created a post with more than 5 votes. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Student 3 months ago, asked a question with at least 3 up-votes. For How to perform edgeR based on serial paired samples? (model.matrix design)
Epic Question 3 months ago, created a question with more than 10,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Popular Question 3 months ago, created a question with more than 1,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Guru 5 months ago, received more than 100 upvotes.
Great Question 11 months ago, created a question with more than 5,000 views. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (Oct 2016)
Gold Standard 17 months ago, created a post with more than 25 bookmarks. For Up-to-date RNA-Seq Analysis Training/Courses/Papers (April 2016)
Popular Question 18 months ago, created a question with more than 1,000 views. For Up-to-date RNA Sequence Analysis Training/Courses/Papers?
Librarian 18 months ago, created a post with more than 10 bookmarks. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Prophet 19 months ago, created a post with more than 20 followers. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
Appreciated 20 months ago, created a post with more than 5 votes. For Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?

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