User: mgrcprof
mgrcprof • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Madrid/ISCII
- Last seen:
- 4 months ago
- Joined:
- 1 year, 4 months ago
- Email:
- m*******@gmail.com
Bioinformatic (Loading...)! Student of a Bioinformatic and Computational Biology MSc program.
Posts by mgrcprof
<prev
• 12 results •
page 1 of 2 •
next >
0
votes
2
answers
579
views
2
answers
... Okey, i will use a shapiro test!
> However, with only three replicates and correction for multiple testing, this approach may not have enough power.
Effectively, after using the t.test as you specified, the number of proteins with a p-val lower than 0.05 is 187, transforming into 0 when applyi ...
written 11 months ago by
mgrcprof • 20
0
votes
2
answers
579
views
2
answers
... Yes, that's exactly what they are, ratios between two conditions. If the data were succesfully centered at 0 i would get the following output from r-base t.test function, no?:
`t.test(data$mean)`
One Sample t-test
data: data$mean
t = 0.25743, df = 3833, p-value = 0.7969
alternative hypothesis: ...
written 11 months ago by
mgrcprof • 20
0
votes
2
answers
579
views
2
answers
... Thank you for your answer Jean-Karim!
I have been taking a look at [R for Proteomics Vignette][1], however i have a problem. This package is designed for the analysis and identification of raw pep files emerging of the analysis. I have a final list of proteins with their ratios. I have transformed ...
written 11 months ago by
mgrcprof • 20
3
votes
2
answers
579
views
5 follow
2
answers
... Hi!
I have received a dataset from an old proteomic experiment which contain the SILAC ratio for 3834 proteins for a determined condition. I'm used to use statistical metrics as the p.value associated to a T-test to establish a cut-off for the consequent over-representation analysis, however, this ...
written 11 months ago by
mgrcprof • 20
0
votes
0
answers
811
views
0
answers
Comment:
A: Drosophila melanogaster assembly
... It's SRA data, i can have several fastq of this type (6 exactly) until reaching a higher coverage. In this case, what assembler do i need to use? the SRA experiment: [SRX078313][1].
[1]: https://www.ncbi.nlm.nih.gov/sra/SRX078313[accn] ...
written 14 months ago by
mgrcprof • 20
0
votes
0
answers
811
views
0
answers
Comment:
C: Drosophila melanogaster assembly
... I have paired-ends reads files (.fastq) each one with ~ 6 million reads with a 74 pb length. ...
written 14 months ago by
mgrcprof • 20
5
votes
0
answers
811
views
6 follow
0
answers
... Hi guys!
I have several questions;
1) Which assembler should I use in order to make a *de novo* assembly of Drosophila melanogaster WGS experiment? I'm not interested in the alignment vs the Ref Genome, I just want to generate the scaffolds/contigs.
2) Does exists an aligner that allows you to ch ...
written 14 months ago by
mgrcprof • 20
4
votes
0
answers
712
views
0
answers
... Hi there!
I'm interested in obtaining the consensus sequence for a determined chromosome in fasta format from the 1000 genomes data. I have bee looking the .bam files that the FTP site provides for each individual (whole sequencing data), however, i am interested in a determined chromosome sequence ...
written 15 months ago by
mgrcprof • 20
0
votes
0
answers
723
views
0
answers
... Hi again!!
I'm trying to obtain the overrepresented pathways within the data set and how do they change under the different conditions. I wonder if exists a tool similar to [IPathwayGuide][1] (but freely avaliable) in the pathway analysis field. Sorry if my question was not well oriented!
Thanks J ...
written 15 months ago by
mgrcprof • 20
1
vote
0
answers
723
views
0
answers
... Hi!
I want to reproduce the results obtained in a paper where the authors generate a group of phosphoproteomics results under different conditions. They used the peak intensities based quantification and a software called [MetaCore][1] (not free) to make a pathway analysis.
I have heard about [IPA ...
written 15 months ago by
mgrcprof • 20
Latest awards to mgrcprof
Autobiographer
15 months ago,
has more than 80 characters in the information field of the user's profile.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 574 users visited in the last hour