User: Marge

gravatar for Marge
Marge280
Reputation:
280
Status:
Trusted
Location:
Italy
Last seen:
6 months, 1 week ago
Joined:
4 years, 8 months ago
Email:
g******@gmail.com

I am currently a bioinformatics post-doc at the Italian Institute of Technology of Genova, Neuroscience and Brain technologies department. My main interest is the using expression profiling as tool to dissect regulatory mechanisms in biological processes associated to development and disease.

Posts by Marge

<prev • 34 results • page 1 of 4 • next >
0
votes
2
answers
3.2k
views
2
answers
Comment: C: ChIPseq - Identical peaks in IP and input samples
... Thank you for the additional explanations! Since you are talking about a transcription factor I would tend to think there was some problem with enriching. An alternative option is that in the experimental conditions you are investigating there is no binding. Or maybe there is cell-specific binding ...
written 2.7 years ago by Marge280
0
votes
2
answers
3.2k
views
2
answers
Answer: A: ChIPseq - Identical peaks in IP and input samples
... Hello, It's quite funny: I am working on a ChIP-seq dataset that seems to share the odd appearance with yours. I have been on these data for a while now, I still don't have The Correct Answers but I can definitely share what I think. One question a-priori would be: what are you trying to ChIP? Is ...
written 2.7 years ago by Marge280
1
vote
0
answers
1.1k
views
0
answers
Comment: C: List of human genes expressed in the brain
... I think that what source to choose and how to define a gene as expressed depends a lot on what you want to do downstream with this information. If you don't worry much about false positives and you are not concerned about genes/transcripts that might be missed with the arrays used, then the approa ...
written 2.7 years ago by Marge280
1
vote
2
answers
868
views
2
answers
Comment: C: Is labeling important as a QC? I dont have any DEG across 8 diets which is reall
... I agree, adding that besides contamination from neighbouring regions, the large variability could also be due to the fact that you have a variety of neuronal types in the hypothalamus that secrete different types of hormones. So in principle you could have a lot of variation if you don't sample exac ...
written 2.7 years ago by Marge280
0
votes
2
answers
897
views
2
answers
Answer: A: Searching for a site or program that can do functional annotation not being blas
... I used gProfiler in the past and I quite like it (comprehensive output, flexible, fast, etc). I am not sure how well it could perform on a 13k input though (in general the set seems a bit on the large side to get informative functional enrichment). ...
written 2.7 years ago by Marge280
2
votes
3
answers
1.8k
views
3
answers
Answer: A: How to identify significant differentially expressed genes and gene regulatory n
... One option I would recommend to investigate co-expression networks changing between the two conditions is the R package WGCNA (Weighted Gene Co-expression Network Analysis). Several tutorials and published application examples are available and there is also very active and informative support. ...
written 2.7 years ago by Marge280
0
votes
0
answers
2.3k
views
0
answers
Comment: C: STAR is taking a LONG time to generate mouse genome
... Did you check if a similar problem was already described in STAR Google Group? I always found solution to aaaall my STAR problems there. Cheers. ...
written 2.8 years ago by Marge280
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Bioinformatician/Bioinformatics Data Analyst, Vienna, Austria
... Thank you very much for the information! ...
written 2.8 years ago by Marge280
3
votes
6
answers
1.8k
views
6
answers
Answer: A: Is microarray gene expression analysis is dead ?
... I don't think microarrays are dead, not yet, for a number of reasons. Despite what WouterDeCoster says, I think they are still cheaper than RNAseq, allowing you more replicates for the same amount of money (so more reliable measurments). It is definitely true that the landscape of what you profil ...
written 2.8 years ago by Marge280
0
votes
1
answer
1.0k
views
1
answers
Comment: C: BLAST not showing any hits
... Just for curiosity: I tried now and it seems to work. Maybe it was only a temporary problem. In general for "Failed" runs I would suggest asking the support of the website. ...
written 2.8 years ago by Marge280

Latest awards to Marge

Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Are we tricking ourselves with batch effect correction?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Are we tricking ourselves with batch effect correction?
Scholar 2.9 years ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Scholar 2.9 years ago, created an answer that has been accepted. For A: Binding sites of annotated chip-seq peak files
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Are we tricking ourselves with batch effect correction?
Autobiographer 3.3 years ago, has more than 80 characters in the information field of the user's profile.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Are we tricking ourselves with batch effect correction?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1462 users visited in the last hour