User: Ahill

gravatar for Ahill
Ahill1.9k
Reputation:
1,880
Status:
Trusted
Location:
United States
Last seen:
2 days, 8 hours ago
Joined:
9 years, 4 months ago
Email:
h********@gmail.com

Posts by Ahill

<prev • 178 results • page 1 of 18 • next >
0
votes
1
answer
84
views
1
answers
Answer: A: Biopython byte positions are not compatible with bgzip
... From the [bgzip man page][1] it looks like the command line bgzip -b option expects zero-based uncompressed offsets. But Bio.bgzf uses virtual offsets, which are not the same as uncompressed offsets. The Bgzf doc [here][2] looks like it may tell you how you can convert between virtual and uncompre ...
written 3 days ago by Ahill1.9k
0
votes
1
answer
196
views
1
answers
Answer: C: negative geo value analysis
... The annotation on this GSM says the reported expression value is: > Normalized signal intensity (Background corrected, log2 transformed, > quantile normalized and base line transformed using the median of all > samples). Since it is a log2-transformed there is nothing intrinsically 'wrong ...
written 5 months ago by Ahill1.9k
0
votes
0
answers
224
views
0
answers
Comment: C: getGEO not returning correct sample names
... FWIW it seems this might be an unexpected skip behavior in readr library's [read_tsv][1] for this particular GSE. Which might be worth reporting at the places recommended in the link above. Presuming you have downloaded and unzipped the series matrix file, using the traditional read.delim in place ...
written 5 months ago by Ahill1.9k
1
vote
0
answers
224
views
0
answers
Comment: C: getGEO not returning correct sample names
... GEOquery documentation here indicates where to report issues: https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html#reporting-problems-or-bugs ...
written 5 months ago by Ahill1.9k
2
votes
2
answers
193
views
2
answers
Answer: A: Code/Tool to locally do sequence alignment
... Yes, you can download, install, and run locally many tools that can match sequences to A. For example, BLAST is available here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download. The best tool to use would depend on your specific requirements. If you want to do pa ...
written 6 months ago by Ahill1.9k
1
vote
1
answer
281
views
1
answers
Answer: A: Problem with merge data while trying to convert gene names
... Your merged data frame `resdata` has zero rows because `theBM` has zero rows. Your retrieval from Biomart failed to return any rows. I would focus on understanding why your ensembl query `getBM(...)` is failing. If your query had returned rows that matched any of the genes in `resdata$genes`, you ...
written 8 months ago by Ahill1.9k
0
votes
1
answer
417
views
1
answers
Answer: A: At which point should I do a log2 transformation of my iTRAQ LCMS data?
... You should take the first approach: log2 transform the ratios, calculate the mean, then subtract ratios. Reasons to prefer that approach are: - log-ratios in data like iTRAQ should be more normally distributed than the raw-data, and so you can comfortably take a simple arithmetic mean of the log- ...
written 10 months ago by Ahill1.9k
0
votes
0
answers
748
views
0
answers
Comment: C: Feature selected-genes vs. differentially expressed genes
... You are certainly right - the GLM approach in DeSeq2 is not a F-test, which would make assumptions of equal variance, etc. that are not made in DESeq2. Assuming you submitted all observed transcripts to the random forest classifier, and not only DESeq2-DE genes, it would be interesting to look at t ...
written 12 months ago by Ahill1.9k
1
vote
0
answers
748
views
0
answers
Comment: C: Feature selected-genes vs. differentially expressed genes
... Yes, to understand differences you would want to compare the differential expression method you've used against the F-test and Gini index methods used by your feature selection, in the context of your experimental design. If this is a one-factor design, for example, and you used ANOVA to select di ...
written 12 months ago by Ahill1.9k
0
votes
0
answers
52
views
0
answers
Comment: C: Multifactor design with Genotype: Is it possible to group all?
... Mods can comment best, but at minimum you can add a direct link to the cross-post here (and vice versa) so that folks know it's in both fora. Like on this post here: https://www.biostars.org/p/322451/#373863. ...
written 14 months ago by Ahill1.9k

Latest awards to Ahill

Scholar 6 months ago, created an answer that has been accepted. For A: What is a Gbase?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Scholar 14 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?
Scholar 14 months ago, created an answer that has been accepted. 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?
Scholar 15 months ago, created an answer that has been accepted. For A: What is a Gbase?
Scholar 19 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 20 months ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Scholar 2.0 years ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For convert MACH .mlprob to Oxford .gen format
Great Question 2.5 years ago, created a question with more than 5,000 views. For Resources for flow cytometry bioinformatics
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Why gene expression data should be log2 transformed?
Scholar 2.8 years ago, created an answer that has been accepted. For A: What is a Gbase?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?
Voter 3.0 years ago, voted more than 100 times.
Centurion 3.0 years ago, created 100 posts.
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What is a Gbase?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1833 users visited in the last hour
_