User: keith.hughitt

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keith.hughitt270
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270
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Location:
United States
Website:
https://github.com/khu...
Twitter:
@KeithHughitt
Last seen:
1 week, 2 days ago
Joined:
6 years, 11 months ago
Email:
k************@gmail.com

about me

Posts by keith.hughitt

<prev • 15 results • page 1 of 2 • next >
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Tool: labnote: A light-weight HTML lab notebook generator
... Greetings, I would like to share a small tool I developed during my graduate work over the past couple years. The software is called "[labnote][1]" and is a simple python-based tool for scanning a Unix-based directory structure and generating a HTML table of contents page for various research outpu ...
notebook jupyter tool labnote rmarkdown reproducible written 2.4 years ago by keith.hughitt270
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Comment: C: Unexpected sample clustering after microarray normalization
... I suspect you are seeing a batch effect. It is not uncommon for differences in batches to explain more of the variance in your data than the biological effects of interest. The fact that there are also differences in the total expression levels differentiating the two groups also supports that idea. ...
written 3.1 years ago by keith.hughitt270
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Answer: A: What is the difference between NZ_ and NC_ identifiers at NCBI?
... From [The NCBI Handbook, ch18][1]: (via [this answer][2]) **NC** - "Complete genomic molecule, usually reference assembly" **NZ** - "Unfinished WGS" [1]: http://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/ [2]: https://www.biostars.org/p/105529/ ...
written 3.2 years ago by keith.hughitt270
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Comment: C: Error in SAMseq analysis with R
... Since the error appears to result from some non-numeric or non-finite values, first thing you might want to try is to check for those in your input counts, e.g.: `sapply(RNA_seq_DNAm, function(x) { sum(is.na(x)) })` for NAs. You can modify this to check for NaN's (`is.nan`) or Infs (`abs(x) == Inf`) ...
written 3.2 years ago by keith.hughitt270
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Comment: C: python: find percentage of match between two sequences
... The [Distance][1] library for Python also has an implementation of hamming distance and some other metrics which I've found useful in the past. [1]: https://pypi.python.org/pypi/Distance/ ...
written 3.2 years ago by keith.hughitt270
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Answer: C: MicroArray Filtering Process/Software?
... You might want to start by checking out the Bioconductor microarray analysis guide: https://www.bioconductor.org/help/workflows/arrays/ ...
written 3.2 years ago by keith.hughitt270
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Comment: C: RNA-seq z-score normalization prior to clustering
... What is the structure of your data, e.g. #samples, #conditions, #replicates/condition? And are you attempting to find clusters of samples? Or genes? Depending on what you are interested in, using z-scores may not be necessary. ...
written 3.2 years ago by keith.hughitt270
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Comment: C: Finding differentially expressed genes between samples from different studies
... Then WouterDeCoster is correct - experiment and cell type are confounded and you cannot reliably detect differences between them. This would only work if you had both cell types for both studies. ...
written 3.2 years ago by keith.hughitt270
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Answer: A: Finding number of duplicates in R
... You can use the `table` function in R to get the count of each duplicated gene. For example, if the gene IDs are stored in a column `gene_id`, you could do: > dat <- data.frame(gene_id=sample(1:3, 20, replace=TRUE), other_col='foo') > table(dat$gene_id) 1 2 3 5 6 9 ...
written 3.2 years ago by keith.hughitt270
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Comment: C: Ribosomal proteins differentially expressed?
... Did you perform any size-factor normalization? It's certainly biologically possible, but in the steps above you don't mention any steps that would adjust for sample size differences. This would also be an easy way in which the differences could appear. ...
written 3.2 years ago by keith.hughitt270

Latest awards to keith.hughitt

Appreciated 19 months ago, created a post with more than 5 votes. For A: Finding number of duplicates in R
Appreciated 21 months ago, created a post with more than 5 votes. For A: Finding number of duplicates in R
Voter 23 months ago, voted more than 100 times.
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Finding number of duplicates in R
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Finding number of duplicates in R
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Proper construction of data matrix for WGCNA (weighted gene coexpression network
Scholar 3.2 years ago, created an answer that has been accepted. For A: Proper construction of data matrix for WGCNA (weighted gene coexpression network
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Proper construction of data matrix for WGCNA (weighted gene coexpression network
Scholar 3.3 years ago, created an answer that has been accepted. For A: Proper construction of data matrix for WGCNA (weighted gene coexpression network
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Proper construction of data matrix for WGCNA (weighted gene coexpression network
Supporter 4.3 years ago, voted at least 25 times.

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