User: newmanss

gravatar for newmanss
newmanss0
Reputation:
0
Status:
New User
Last seen:
1 year, 4 months ago
Joined:
4 years, 5 months ago
Email:
n*******@pbrc.edu

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by newmanss

<prev • 16 results • page 2 of 2 • next >
0
votes
1
answer
849
views
1
answer
DESeq2 design matrix for normal & enriched samples
... Hello, I am working with a dataset composed of three treatment groups.  I have paired samples that consist of a baseline sample and the same sample which has been enriched for active transcription.  The batch variable accounts for batches during sample preparation. The experimental design looks lik ...
deseq2 multiple factor design written 4.1 years ago by newmanss0 • updated 4.1 years ago by Michael Love23k
0
votes
1
answer
1.3k
views
1
answers
Comment: C: ShortRead- how to edit the id in a fastq
... Thank you.  I will try that strategy.  A moment ago, before I checked for an answer, I tried one more approach that appears to work.  fqr@id[ ] <- sub(" ",barcodestr, ShortRead::id(fqr)) then to check- head(fqr@id) A BStringSet instance of length 6 width seq [1] 72 M00967:43:0000000 ...
written 4.3 years ago by newmanss0
0
votes
1
answer
1.3k
views
1
answer
ShortRead- how to edit the id in a fastq
... I need to edit the fragment IDs in a MiSeq fastq file. I'm using ShortRead to load the fastq and I've successfully managed to insert the substring needed  but I can't use my code to substitute the new ID into the id slot of my fastq.  Here is my current code: fqr <- sub(" ",barcodestr, ShortRead ...
shortread written 4.3 years ago by newmanss0 • updated 4.3 years ago by Valerie Obenchain6.7k
0
votes
3
answers
2.9k
views
3
answers
Answer: A: DESeq2 design model for treatment analysis controlling for age and sex
... Dear Michael, I selected an Age cutoff, median of the overlapping ages for the groups male and female.  I used cut() successfully but when the DESeq() analysis was running, it halted with this error: Error in optim(betaRow, objectiveFn, method = "L-BFGS-B", lower = -large, : L-BFGS-B needs finite ...
written 4.4 years ago by newmanss0
0
votes
3
answers
2.9k
views
3
answers
Answer: A: DESeq2 design model for treatment analysis controlling for age and sex
... Thank you for a very clear outline and explanation of the process steps.  For the age cut, can you provide more detail as to selecting the cut point since there is a lot of overlap between the phenotype groups.  Do I just disregard phenotype and let it cut between young and old or should I look at t ...
written 4.4 years ago by newmanss0
1
vote
3
answers
2.9k
views
3
answers
DESeq2 design model for treatment analysis controlling for age and sex
... Hello, I am an inexperienced user and in my searching haven't found a clear example to this basic question.  My experiment design is comprised of male and female subjects of varying ages grouped by treatment response, flexible and inflexible factors.  The mean age is significantly different between ...
deseq2 design and contrast matrix written 4.4 years ago by newmanss0

Latest awards to newmanss

Popular Question 2.6 years ago, created a question with more than 1,000 views. For DESeq2 design model for treatment analysis controlling for age and sex

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 292 users visited in the last hour