User: Ahill
Ahill • 900
- Reputation:
- 900
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 11 hours ago
- Joined:
- 5 years, 8 months ago
- Email:
- h********@gmail.com
Posts by Ahill
<prev
• 81 results •
page 1 of 9 •
next >
0
votes
0
answers
172
views
0
answers
... Or [GEO][1], [Expression Atlas][2]?
[1]: https://www.ncbi.nlm.nih.gov/gds?term=breast%20estrogen%20positive&cmd=correctspelling
[2]: https://www.ebi.ac.uk/gxa/query?geneQuery=%5B%5D&organism=homo%20sapiens&conditionQuery=%5B%7B%22value%22%3A%22breast%20cancer%20cell%20line%22%7D%5D ...
written 3 months ago by
Ahill • 900
0
votes
0
answers
185
views
0
answers
... What type of microarray and normalization methods? For oligo microarrays (e.g. Affymetrix) - generally no. Hybridization intensities can be probe-sequence dependent, so if Gene A has an intensity of 10 and Gene B has intensity 20, it would be very risky to to conclude B is expressed at twice the l ...
written 4 months ago by
Ahill • 900
3
votes
1
answer
385
views
1
answers
... When it is used, a main rationale for log-transformation is heteroskedasticity. The variance of expression measurements on many platforms (arrays, etc.) depends on the expression level. By log-transforming, you reduce this dependence and your data becomes better-behaved for statistical testing. A ...
written 4 months ago by
Ahill • 900
1
vote
1
answer
170
views
1
answers
Comment:
C: miRNA-Gene Interaction P-Values
... Apparently no. The authors say "[the pCT] reflected the Bayesian estimate of the probability that a site is conserved due to selective maintenance of miRNA targeting rather than by chance or any other reason not pertinent to miRNA targeting". So this is definitely not a type I error measure like a ...
written 4 months ago by
Ahill • 900
1
vote
1
answer
170
views
1
answers
... TargetScan provides a database of miRNA-gene interactions including a pCT statistic for the interactions. For human, downloadable from here: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert71.cgi ...
written 4 months ago by
Ahill • 900
2
votes
1
answer
186
views
1
answers
... Not a geneticist, but using your notation, for autosomes 2p is the expected (mean) value of x and sqroot(2p(1-p)) will be the standard deviation of x. So this is a [z-score][1]. The standardized values (wij) will have mean zero and variance 1 for each SNP, I guess a nice property for some calculat ...
written 4 months ago by
Ahill • 900
0
votes
1
answer
253
views
1
answers
Answer:
A: SNPRelate data file
... Instructions to create a GDS file: http://corearray.sourceforge.net/tutorials/SNPRelate/#create-a-gds-file-of-your-own ...
written 5 months ago by
Ahill • 900
0
votes
1
answer
289
views
1
answers
... Just speculating, but two approaches to select a control gene set would be selection of "known" housekeeping genes (e.g. GAPDH, Actin, etc.), or rank invariant set normalization to select genes whose ranks are stable across samples (original ref I believe at https://www.ncbi.nlm.nih.gov/pmc/articles ...
written 5 months ago by
Ahill • 900
0
votes
1
answer
402
views
1
answers
... Interested in responses on this. I'd think fundamentally there is no way to reliably infer risk allele given only p/odds ratio for a SNP. I think it's a common, but not certainly not universal, convention that the minor allele is used as effect allele in common software used to compute association ...
written 6 months ago by
Ahill • 900
0
votes
0
answers
260
views
0
answers
... In immunophenotyping, some common goals are to either quantify the number of cells in previously defined cell populations, or to identify new, previously unknown groups of cells that correlate with a response of interest. In both those cases, "bioinformatics" approaches for supervised and unsupervi ...
written 7 months ago by
Ahill • 900
Latest awards to Ahill
Prophet
8 months ago,
created a post with more than 20 followers.
For Resources for flow cytometry bioinformatics
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: So what counts as a "novel" classifier?
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Resources for flow cytometry bioinformatics
Supporter
2.7 years ago,
voted at least 25 times.
Appreciated
3.0 years ago,
created a post with more than 5 votes.
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: 466 users visited in the last hour