User: mgrcprof
mgrcprof • 20
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Bioinformatic (Loading...)! Student of a Bioinformatic and Computational Biology MSc program.
Posts by mgrcprof
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... 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 9 weeks ago by
mgrcprof • 20
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... 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 9 weeks ago by
mgrcprof • 20
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... 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 9 weeks ago by
mgrcprof • 20
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... 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 9 weeks ago by
mgrcprof • 20
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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 5 months ago by
mgrcprof • 20
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Comment:
C: Drosophila melanogaster assembly
... I have paired-ends reads files (.fastq) each one with ~ 6 million reads with a 74 pb length. ...
written 5 months ago by
mgrcprof • 20
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... 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 5 months ago by
mgrcprof • 20
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... 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 6 months ago by
mgrcprof • 20
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... 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 6 months ago by
mgrcprof • 20
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... 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 6 months ago by
mgrcprof • 20
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