User: Caleb Bostwick

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3 months, 3 weeks ago
Joined:
5 years, 3 months ago
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b*******@ufl.edu

Posts by Caleb Bostwick

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Analyze time course experiment with multiple samples from multiple animals with DESeq2
... Hello, I am a graduate student who would like to know if I am designing my differential expression experiment correctly using DESeq2. I performed RNA-seq on tissues originating from 14 total animals at 4 time points of exposure to a drug. 3 animals were exposed for 0 hours (no exposure; control), 3 ...
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Comment: C: DESeq2 Error in estimateSizeFactorsForMatrix
... Hello Michael. I generated the rowSums count and got: > table(rs) rs 4 18820 I think I have 18820 rows (genes) in my data and 4 samples, so as suggested by the original error, it appears all my genes have 0's for their counts. I displayed my ddsFull object data below for reference: > dd ...
written 5.3 years ago by Caleb Bostwick30
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DESeq2 Error in estimateSizeFactorsForMatrix
... Thank you for your quick reply Simon. I am inexperienced with R and do not know how to check if all my genes contain a zero in at least one of the samples. I'm sorry for my ignorance, but if someone would explain or point me to an explanation of how I could check this, I will certainly check this. H ...
alignment deseq2 written 5.3 years ago by Caleb Bostwick30 • updated 5.3 years ago by Michael Love25k
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Answer: A: DESeq2 Error in estimateSizeFactorsForMatrix
... Hello Michael. I am a neuroscience researcher attempting to use the DESeq2 package to perform differential expression analysis of my sequencing data. I am following the beginner vignette but substituting my own data into the code. I managed to get to the part where it tells me to call the DESeq func ...
written 5.3 years ago by Caleb Bostwick30

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Popular Question 2.2 years ago, created a question with more than 1,000 views. For DESeq2 Error in estimateSizeFactorsForMatrix

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