User: Ahill
Ahill • 1.3k
- Reputation:
- 1,270
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 13 hours ago
- Joined:
- 7 years, 1 month ago
- Email:
- h********@gmail.com
Posts by Ahill
<prev
• 121 results •
page 1 of 13 •
next >
0
votes
1
answer
99
views
1
answers
... The .cel files are the almost-most-raw intensity data, and contain the probeset-level intensities from the array. So (for example) if there were 11 probe-pairs per probeset on the array, the .cel file would contain 22 intensities per probeset.
According to the GEO page you linked, the data table a ...
written 10 days ago by
Ahill • 1.3k
0
votes
1
answer
102
views
1
answers
Answer:
A: Query based on PMIDs
... The [NCBI elink utility][1] will take a list of PMIDs as input and map to GEO GDS, or SRA accessions. For example, here are 2 PMIDs that each have one associated GEO GDS:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&db=gds&id=15772128&id=24808371
This call re ...
written 12 days ago by
Ahill • 1.3k
0
votes
2
answers
328
views
2
answers
... You could reach out to an open source bioinformatics project that could use experienced developer help. This earlier post had listed a few examples [https://www.biostars.org/p/130126/][1] but I'm sure others can offer many more ideas.
[1]: https://www.biostars.org/p/130126/ ...
written 5 weeks ago by
Ahill • 1.3k
1
vote
1
answer
190
views
1
answers
... It can be valid to use PC scores as the independent variables in linear models, instead of the underlying primary variables. For predicting a binary outcome like disease/healthy, you could look at a lm() logistic model like:
disease.status ~ PC1 + PC2 + ...
Of course, the usefulness of this w ...
written 5 weeks ago by
Ahill • 1.3k
0
votes
1
answer
190
views
1
answers
... Are you looking to predict your Target Variable (disease/healthy) from the clinical and genomic data? It sounds like you have labeled training data where the disease/healthy classification is known. If so, you might want to use supervised approaches to do feature selection, rather than unsupervise ...
written 5 weeks ago by
Ahill • 1.3k
1
vote
1
answer
168
views
1
answers
... If searching for PF00502 domain by BLASTP, you may need to be careful that your hits are true positives for this domain, since the domain has variability. If your 13 genomes are curated in UniProt, and what you need to find is the all the proteins in the genome that match the domain, one alternativ ...
written 6 weeks ago by
Ahill • 1.3k
0
votes
1
answer
197
views
1
answers
... The chromsome X sequence was assembled from genomic DNA fragments that were packaged into fosmids. In this case, your fosmid (FO081428.1) was one of a number of fosmids that were assembled together to form the inferred chromosome X sequence (NC_003284.9). So this is not a contamination - in fact t ...
written 9 weeks ago by
Ahill • 1.3k
1
vote
1
answer
233
views
1
answers
... You mentioned you are running on a linux cluster. What job management system are you using? How many fastq files (elements in ${cells[@]})? If more than one,can you simply unroll your for loop, which runs each $cell serially, and execute a set of simultaneous jobs that will run in parallel, one p ...
written 12 weeks ago by
Ahill • 1.3k
0
votes
0
answers
114
views
0
answers
... The longer list of 6007 genes shown at the link you provided appears to include multiple other phenotypes and species, and an export filtered to "Homo sapiens" yields 10,396 genes, which makes me question the interpretation of this interface. You may want to query the site owners or their documenta ...
written 12 weeks ago by
Ahill • 1.3k
0
votes
2
answers
180
views
2
answers
... I'll add that one consideration driving the number of probe-pairs per probe-set in later Affymetrix designs was the desire to query more transcripts in the same amount of silicon real estate, given the fixed size (in square microns) of each probe feature, which was determined by the resolution of th ...
written 3 months ago by
Ahill • 1.3k
Latest awards to Ahill
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For convert MACH .mlprob to Oxford .gen format
Great Question
11 weeks ago,
created a question with more than 5,000 views.
For Resources for flow cytometry bioinformatics
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Why gene expression data should be log2 transformed?
Appreciated
4 months ago,
created a post with more than 5 votes.
For A: Why gene expression data should be log2 transformed?
Voter
9 months ago,
voted more than 100 times.
Centurion
9 months ago,
created 100 posts.
Guru
11 months ago,
received more than 100 upvotes.
Librarian
15 months ago,
created a post with more than 10 bookmarks.
For Resources for flow cytometry bioinformatics
Prophet
2.1 years ago,
created a post with more than 20 followers.
For Resources for flow cytometry bioinformatics
Commentator
2.4 years ago,
created a comment with at least 3 up-votes.
For C: So what counts as a "novel" classifier?
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Resources for flow cytometry bioinformatics
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 667 users visited in the last hour