User: Alex Gibbs

gravatar for Alex Gibbs
Alex Gibbs40
Reputation:
40
Status:
New User
Location:
Cardiff University
Last seen:
1 week, 6 days ago
Joined:
2 years, 10 months ago
Email:
g*****@cardiff.ac.uk

I am a first-year PhD student at Cardiff University focusing my studies on the cancer stem cell basis of metastatic skin cancer. KESS2 East Studentship recipient working alongside Skin Care Cymru and Aneurin Bevan University Health Board. I have around 2 years of bioinformatics experience ranging from Microarray and RNA-Seq analysis and R.

Posts by Alex Gibbs

<prev • 10 results • page 1 of 1 • next >
0
votes
0
answers
114
views
0
answers
Comment: C: Combining Samples in Microarray Analysis
... Yes, you are correct! I completely forgot about performing group-wise comparisons within Limma, thanks for bringing that up. I will do this instead. ...
written 8 weeks ago by Alex Gibbs40
3
votes
1
answer
173
views
1
answers
Answer: A: i need to find a database
... You could try using [PubMed's 'Advanced Search'](https://www.ncbi.nlm.nih.gov/pubmed/advanced) a try. All you need to do is plug in the cpg island you are looking for into the search box and then in the dropdown menu to the left, select to search for this cpg island in the title, abstract or all fi ...
written 8 weeks ago by Alex Gibbs40 • updated 8 weeks ago by RamRS25k
1
vote
0
answers
114
views
0
answers
Combining Samples in Microarray Analysis
... Hi all, I have 3 disease groups that I would like to compare. Each disease group has 3 samples. Illumina microarray has been performed on each sample along with matched controls. I have generated 9 DEG files for each sample (Affected 1A vs Control, Affected 1B vs Control, Affected 1C vs Control et ...
microarray sequencing written 8 weeks ago by Alex Gibbs40
1
vote
1
answer
155
views
1
answers
Comment: C: Microarray Heatmap with DEG's
... Thank you very much, Kevin! I will give this a go! ...
written 10 weeks ago by Alex Gibbs40
2
votes
1
answer
155
views
1
answer
Microarray Heatmap with DEG's
... Hi all! I have generated 18 DEG files which consist of 23,835 genes each (7x Affected_v_Control, 7x Affected_v_Control2, 4x Control_v_Control2). I haven’t filtered these files for Adj.P or LogFC yet. I have then opened these up in Excel and ordered them by probe ID, then taken the LogFC values and ...
R microarray illumina written 10 weeks ago by Alex Gibbs40 • updated 10 weeks ago by Kevin Blighe52k
4
votes
0
answers
198
views
0
answers
How to find transcription factor downstream binding
... Hi all, I would like to find out what the mouse Stat3 transcription factor **binds** to and the full signalling pathway(s) that it is involved in. So far, I have only managed to find a signalling pathway that ends in Stat3, and subsequently genes that bind to Stat3. I have tried JASPAR, but the w ...
gene rna-seq written 8 months ago by Alex Gibbs40 • updated 6 months ago by Biostar ♦♦ 20
2
votes
1
answer
719
views
1
answer
GSEA with mouse RNAseq data
... Hi everyone, I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software. I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 sign ...
rna-seq written 9 months ago by Alex Gibbs40 • updated 9 months ago by Buffo1.7k
0
votes
1
answer
345
views
1
answers
Comment: C: E coli Sequencing & Analysis
... Thank you very much for your reply! I think I will try both methods (SPades&Prokka, NCBI tools) and see which ones I get on with most. ...
written 13 months ago by Alex Gibbs40
2
votes
1
answer
345
views
1
answer
E coli Sequencing & Analysis
... Hello, I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc. The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with 150bp paired end reads. The 'raw' files that I have is the forward and reverse reads. I have i ...
genome assembly alignment sequencing written 13 months ago by Alex Gibbs40 • updated 12 months ago by rebeccarenberg20
0
votes
0
answers
802
views
0
answers
Remove Probes from Raw .CEL Files - AFFY HG-U133-Plus2.0
... Hi all, I have multiple Accessions(13) that I'm combining to analyse data(~2000 samples). All of the Accessions have the same platform (GPL570). After investigating all the Accessions, I noticed that one of them (E-MTAB-3444) has around 300 extra probes added to the platform. This means that I can ...
R rna-seq written 2.9 years ago by Alex Gibbs40

Latest awards to Alex Gibbs

Scholar 8 weeks ago, created an answer that has been accepted. For A: i need to find a database
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: i need to find a database
Autobiographer 8 weeks ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2029 users visited in the last hour