User: Gotgenes

gravatar for Gotgenes
Gotgenes430
Reputation:
430
Status:
Trusted
Location:
Bethesda, MD, USA
Website:
http://gotgenes.com/
Last seen:
4 years, 3 months ago
Joined:
8 years, 8 months ago
Email:
c***********@gmail.com

My name is Chris Lasher. I'm a postdoctoral fellow at NCBI. I enjoy revision control, unit testing, and long coding sessions in Python.

Posts by Gotgenes

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Dbsnp132 1000Genomes Vcf File Info Field: Bitfield Structure
... I also wonder why the answer's author feels the need to reverse the bits. My best guess is that he is unfamiliar with the convention that, these days, bit ordering is typically most significant bit first. This is the convention followed in Python; for example, try for i in range(9): print(i, b ...
written 4.3 years ago by Gotgenes430
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Comment: C: An Easy Way To Permute/Randomise Biological Networks?
... This works, but note that randomizing node IDs will not preserve the degree distribution for the gene/protein/molecule, only for the network as a whole. In other words, if you started with 2 genes gene a and gene b that had 10 neighbors, there will still be 2 genes with 10 neighbors after randomizat ...
written 6.5 years ago by Gotgenes430
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Answer: A: An Easy Way To Permute/Randomise Biological Networks?
... Here is an implementation in Python excerpted from code I wrote for my dissertation. (I apologize for not posting it directly here on BioStars, but the code exceeded the character limit here.) The relevant method is EdgeSwapGraph.randomize_by_edge_swaps(). The algorithm is straightforward and should ...
written 6.5 years ago by Gotgenes430
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Comment: C: Transcriptome Microarray Database
... Your question is ambiguous because of the mix of wording. Transciptomes, microarrays, and ESTs are all separate, albeit related, concepts and techniques. A transcriptome is all RNA transcriptions of genes in a genome; microarrays measure the expression of a subset of the transcriptome; ESTs are sequ ...
written 7.4 years ago by Gotgenes430
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Limma Design And Contrast Matrices For Two-Color (Two-Channel) Data With Common Biological Reference, Not Common Mrna Reference
... This question is related to a question I asked here earlier. Since then, I have gotten the raw data and processed it into normalized MA values. I'll repeat the background and motivation below. The study GSE13465 contains experiments of toxic effects of acetaminophen on two organisms: human rat ...
gene bioconductor limma microarray written 7.4 years ago by Gotgenes430 • updated 4.9 years ago by Biostar ♦♦ 20
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Answer: A: Data Mining Or Bioinformatics?
... I would suggest instead first looking for professors whose groups do data mining with medical or biological research, then worrying about what the degree will say. There are two types groups which you should look for, and which could both lead to a satisfactory experience. The first type of group is ...
written 7.4 years ago by Gotgenes430
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Comment: C: Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
... I'm accepting this answer, summarized simply as, "Don't use GEOquery to obtain gene expression measurements; use raw data." GEOquery is nice for grabbing meta-information and information about the platform probes, but the expression data deposited in GEO is a complete grab-bag and requires close scr ...
written 7.4 years ago by Gotgenes430
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Comment: C: Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
... @David I arrived at the same conclusion; I kept checking back at Biostar but for whatever reason didn't get a notification that you added your comment. Thanks for your selfless sleuthing. ...
written 7.4 years ago by Gotgenes430
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Comment: C: Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
... I'm actually guessing they're ImaGene files based on the limma User's Guide stating, "ImaGene stores red and green intensities in separate files," (Section 4.3, page 16 of the PDF as of limma v.3.8.2), there being separate Cy3 and Cy5 files in the supplementary material of the GSMs, and the VALUE de ...
written 7.4 years ago by Gotgenes430
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Comment: C: Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
... David, it's helpful to know that using the raw data is preferable. The raw expression files are available separately for the Cy5 and Cy3 data for each of the samples (e.g. see http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM339445 ) whereas the limma User's Guide describes scenarios when the Cy ...
written 7.4 years ago by Gotgenes430

Latest awards to Gotgenes

Appreciated 4.3 years ago, created a post with more than 5 votes. For Locations Of Plots Of Quantities Of Publicly Available Biological Data
Appreciated 6.0 years ago, created a post with more than 5 votes. For Locations Of Plots Of Quantities Of Publicly Available Biological Data
Good Question 6.0 years ago, asked a question that was upvoted at least 5 times. For Locations Of Plots Of Quantities Of Publicly Available Biological Data
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Locations Of Plots Of Quantities Of Publicly Available Biological Data
Supporter 6.0 years ago, voted at least 25 times.
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: An Easy Way To Permute/Randomise Biological Networks?
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Data Mining Or Bioinformatics?
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Locations Of Plots Of Quantities Of Publicly Available Biological Data
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Best Resources To Learn Molecular Biology For A Computer Scientist.
Student 6.0 years ago, asked a question with at least 3 up-votes. For Limma Analysis For Two-Channeled Microarray Data Fetched Using Geoquery
Student 6.0 years ago, asked a question with at least 3 up-votes. For Locations Of Plots Of Quantities Of Publicly Available Biological Data
Autobiographer 6.0 years ago, has more than 80 characters in the information field of the user's profile.

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