User: Delasa Aghamirzaie

Reputation:
70
Status:
Trusted
Location:
United States
Last seen:
4 years, 8 months ago
Joined:
6 years, 6 months ago
Email:
d*****@vt.edu

Posts by Delasa Aghamirzaie

<prev • 9 results • page 1 of 1 • next >
0
votes
2
answers
4.0k
views
2
answers
Answer: A: Limma for RNA-seq data
... Thanks for your response. Just a quick question: Is taking logs a necessary step for this analysis (if I choose to use Limma for FPKM values)? That would result INF in case of FPKM = 0. Is that internally handled in Limma?  ...
written 4.7 years ago by Delasa Aghamirzaie70
5
votes
2
answers
4.0k
views
2
answers
Limma for RNA-seq data
... Hello, I am happy to see that Limma is updated to handle RNA-Seq data. I have FPKM values for my transcripts. Can I use them directly as input to Limma? Is there any kind of normalization to do on FPKM values prior to using Limma?  Thanks, Delasa ...
limma written 4.7 years ago by Delasa Aghamirzaie70
0
votes
0
answers
569
views
0
answers
Protein domain identification using bioconductor packages
... Hi, I was wondering if there is any bioconductor package that does translation for a given set of sequences and then is capable of identifying protein domains in those translated sequences? Delasa Aghamirzaie Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student Virginia Tech Black ...
written 6.2 years ago by Delasa Aghamirzaie70
0
votes
1
answer
871
views
1
answer
Start and End positions in the GTF/GFF3 files
... Hi Bioconductors, I have a question regarding to GTF/GFF3's start and end positions in the genome and I dont know if here is the right place to ask. I would be appreciated if anyone can answer my question. Does anybody know the numbers regarding to start position and end positions in GTF/GFF3 files ...
written 6.4 years ago by Delasa Aghamirzaie70 • updated 6.4 years ago by Hervé Pagès ♦♦ 14k
0
votes
1
answer
878
views
1
answers
Comment: C: CummeRbund multiple cases
... Hi Loyal, Thanks alot for your great tool, Cummerbund. I have used "tuxedo suit" tools for analyzing my RNA-seq data. I was wondering if there is any facility in Cummerbund to visualize the isoforms and splicing events. For example: for each gene showing us different exons and introns in known isofo ...
written 6.5 years ago by Delasa Aghamirzaie70
0
votes
2
answers
3.1k
views
2
answers
Comment: C: p-value vs adjusted p-value in DEXSeq
... Dear Simon, Thanks a lot for your prompt response and also the link. Sincerely Yours, Delasa Aghamirzaie Genetics, Bioinformatics, and Computational Biology (GBCB) PhD Student Virginia Tech Blacksburg, Virginia On Wed, Jun 19, 2013 at 1:20 PM, Simon Anders wrote: > Hi Delasa > > > ...
written 6.5 years ago by Delasa Aghamirzaie70
0
votes
2
answers
3.1k
views
2
answers
p-value vs adjusted p-value in DEXSeq
... Hi, I have used DEXSeq for differential exon usage testing. I believe what DEXSeq uses as threshold for finding significant differentially expressed exons is p-adjust < 0.1 and it reports both p-value and p-adjust in its results. My question is that what is the difference between p-adjust and p-v ...
dexseq written 6.5 years ago by Delasa Aghamirzaie70 • updated 6.5 years ago by Simon Anders3.6k
0
votes
0
answers
1.2k
views
0
answers
DEXSeq, looking for a clever way for interpretation of results
... Hi Alejandro / Simon I have done DEXSeq for testing differential exon usage in my time course RNA-seq data (10 time points). I have some problems in analyzing/interpreting the results of DEXSeq and I would be appreciated if you could help me find my answers. I have tested differential exon usage u ...
annotation go dexseq written 6.5 years ago by Delasa Aghamirzaie70
0
votes
1
answer
1.5k
views
1
answer
Detecting differential usage of introns from RNA-seq data.
... Hi Alejandro, I was reading the messages between you and Fong for testing differential intron usage. I am interested in finding intron retention events in my data as well, since intron retention is the most frequent splicing event in plants rather than exon skipping. I have already did DEXSeq for ...
preprocessing dexseq written 6.5 years ago by Delasa Aghamirzaie70 • updated 6.5 years ago by Alejandro Reyes1.7k

Latest awards to Delasa Aghamirzaie

Popular Question 4.7 years ago, created a question with more than 1,000 views. For Detecting differential usage of introns from RNA-seq data.
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Limma for RNA-seq data
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Limma for RNA-seq data
Popular Question 4.7 years ago, created a question with more than 1,000 views. For p-value vs adjusted p-value in DEXSeq

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 366 users visited in the last hour