User: Ahill

gravatar for Ahill
Ahill1.5k
Reputation:
1,480
Status:
Trusted
Location:
United States
Last seen:
1 day, 3 hours ago
Joined:
7 years, 8 months ago
Email:
h********@gmail.com

Posts by Ahill

<prev • 146 results • page 1 of 15 • next >
0
votes
0
answers
130
views
0
answers
Comment: C: Subread alignment issue
... What operating system are you on? Did you install from a precompiled binary matched to your OS, or from from source? Have you tried posting to the support site or user group linked from the [subread home page][1]? Those contacts might be best source of help for a malloc error like this one. [ ...
written 7 weeks ago by Ahill1.5k
0
votes
0
answers
210
views
0
answers
Comment: C: Mean-variance trend in voom
... Rays on these types of plots extending from very low counts can sometimes be due to discretization of small integer counts (e.g, 0.5+0,1,2,3, ...) and variances particularly if n is small. How many replicates do you have included the mean/variance estimates? You could grab the source data from the ...
written 10 weeks ago by Ahill1.5k
2
votes
2
answers
322
views
2
answers
Comment: C: Is there a HGNC symbol or any ENSEMBLE/RefSeq ID for this UniProt : Rheumatoid
... Interesting... I see the source of the Uniprot entry seems to be automated translation of the cDNA you linked from [this 1993 pub][1] (see figure 1). Paper suggests chain encoded by "HK102", a vK1 chain gene (as it was named in 1993?). There are many high-homology hits to this cDNA sequence in the ...
written 10 weeks ago by Ahill1.5k
0
votes
0
answers
189
views
0
answers
Comment: C: Differential gene expression analysis: how different could be the number of samp
... I see this issue has been raised on bioconductor (e.g. [here][1]). Not a statistician and interested to hear other views, but I'd say the DE methods in DESeq2 are valid for unbalanced groups; but they may be less optimal than if you had a balanced design with the same total sample size. You have a ...
written 11 weeks ago by Ahill1.5k
1
vote
1
answer
168
views
1
answers
Comment: C: Looking for tool recommendations for text mining
... If you are looking for precomputed gene or protein level interactions from text mining, have you seen [iHOP][1]? I've not looked at in quite a while but they did curate from PubMed "28.4 million sentences and 110,000 genes from over 2,700 organisms". [1]: https://en.wikipedia.org/wiki/Informati ...
written 11 weeks ago by Ahill1.5k
0
votes
0
answers
244
views
0
answers
Comment: C: removing confounding batch effect with RUVseq
... You mentioned "two types of treatments". If there is a third factor "treatment" in addition to time and batch that is not shown in the design matrix above can you add it? Colleagues have have had some good experience with `RUVg` in general but I'm not clear that your design matches their experienc ...
written 12 weeks ago by Ahill1.5k
0
votes
0
answers
180
views
0
answers
Comment: C: Identifying genes associated with a binary classification for many cell lines
... Ah, OK. If 'biological.phenomenom' is a binary label on each cell line (not an experimental factor that you modulated) then I suppose very confounded with cell.line effects. If cell.line effects are large (probably) but there are still 'biological.phenomenom' main effects that are large enough to ...
written 3 months ago by Ahill1.5k
0
votes
0
answers
180
views
0
answers
Comment: C: Identifying genes associated with a binary classification for many cell lines
... You describe that you are interested in finding genes most associated with the binary classification (versus building a predictor of your binary class?). If this is a gene selection question, I would think one alternative would be a differential expression approach: i.e. limma or equivalent with yo ...
written 3 months ago by Ahill1.5k
1
vote
0
answers
250
views
0
answers
Comment: C: Dunn Index for Clusters from scRNA-Seq
... What about comparing the Louvain modularity scores across your different k values? In principle, Dunn index can be applied to assess clustering results for any method that groups items, presuming you can compute distances between the items. Calculating the Dunn index on your clusters would tell yo ...
written 3 months ago by Ahill1.5k
4
votes
1
answer
233
views
1
answers
Answer: C: Microarray RMA_log2Signal fold change calculation
... Yes, given the types you describe. RMA is on the log-2 scale. You've correctly calculated the fold change. 832 is a very big fold change, so might be very surprising but perhaps not impossible, depending on what your gene is and what the experimental conditions are. I'd agree that it is risky to ...
written 3 months ago by Ahill1.5k

Latest awards to Ahill

Scholar 3 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Popular Question 7 months ago, created a question with more than 1,000 views. For convert MACH .mlprob to Oxford .gen format
Great Question 9 months ago, created a question with more than 5,000 views. For Resources for flow cytometry bioinformatics
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Scholar 13 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Voter 15 months ago, voted more than 100 times.
Centurion 16 months ago, created 100 posts.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Guru 18 months ago, received more than 100 upvotes.
Librarian 21 months ago, created a post with more than 10 bookmarks. For Resources for flow cytometry bioinformatics
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 2.3 years ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Prophet 2.6 years ago, created a post with more than 20 followers. For Resources for flow cytometry bioinformatics
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: So what counts as a "novel" classifier?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 3.5 years ago, created an answer that has been accepted. For A: What is a Gbase?
Scholar 3.6 years ago, created an answer that has been accepted. For A: What is a Gbase?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Resources for flow cytometry bioinformatics

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1015 users visited in the last hour