Showing : Proteomics • reset
25
votes
9
replies
6.8k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 40
8
votes
2
replies
2.8k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts proteomics limma edger deseq
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 70
8
votes
0
replies
3.6k
views
Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
8.8 years ago Martin Morgan 25k
6
votes
6
replies
1.6k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 10
5
votes
3
replies
1.8k
views
Strong upwards correlation between log fold change and average log expression in MD plot of Limma
limma proteomics
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
5
votes
6
replies
1.4k
views
possible package naming conflict
proteomics
3.4 years ago Tobias ▴ 40
5
votes
6
replies
3.7k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics NPX limma
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 10
4
votes
9
replies
2.2k
views
Limma is doing the right way to calculate the fold change?
limma proteomics
updated 6.9 years ago by 1.6k • written 6.9 years ago by ▴ 30
4
votes
5
replies
2.0k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 5.2 years ago by 1.6k • written 5.2 years ago by ▴ 10
3
votes
0
replies
2.2k
views
Job: Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job proteomics Job statistics
4.5 years ago • updated 4.3 years ago Gordon Smyth 50k
3
votes
3
replies
1.3k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 15 months ago by 50k • written 15 months ago by • 0
3
votes
4
replies
1.8k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
3
votes
4
replies
1.3k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 5.5 years ago by ▴ 80 • written 5.5 years ago by • 0
3
votes
2
replies
1.5k
views
DEP: Grouping Samples for missing value imputation
DEP missing value imputation proteomics rforproteomics
6.4 years ago • updated 6.2 years ago alex.gos90 ▴ 10
3
votes
3
replies
1.1k
views
Clarification of results tables in DEP
DEP proteomics
updated 4.7 years ago by ▴ 70 • written 4.8 years ago by ▴ 490
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.0k • written 6.3 years ago by • 0
3
votes
1
reply
2.2k
views
Tutorial: Mass Spectrometry Data Analysis with the Spectra Package
mass spectrometry proteomics metabolomics Tutorial
written 3.5 years ago by ★ 2.0k
2
votes
0
replies
2.3k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
4.6 years ago Laurent Gatto 1.6k
2
votes
2
replies
856
views
Where can I get functional bins for Arabidopsis thaliana genome (AGIs)
r proteomics RNA-Seq
updated 5.1 years ago by ▴ 180 • written 5.1 years ago by ▴ 10
2
votes
7
replies
1.5k
views
I get nothing in my up and down regulated genes
limma proteomics label free
7.7 years ago Nemo ▴ 80
2
votes
0
replies
1.2k
views
mapping protein PTM data
proteomics
6.4 years ago petyuk ▴ 70
2
votes
12
replies
1.6k
views
msmsTests, NA values in test.results output
Proteomics msmstests FDR
updated 5.5 years ago by 1.6k • written 5.5 years ago by • 0
2
votes
5
replies
1.7k
views
proteomics analysis
Proteomics analysis
updated 21 months ago by ▴ 90 • written 21 months ago by • 0
2
votes
0
replies
1.2k
views
News: LAST CHANCE: May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
news proteomics course training msstats News
6.2 years ago mnchoi67 ▴ 40
2
votes
4
replies
1.5k
views
how to find up regulated proteins from a label free
deseq2 proteomics label free
updated 7.7 years ago by 1.6k • written 7.7 years ago by ▴ 80
2
votes
1
reply
983
views
Extremely low P-values when using Limma on high sample size proteomics data
limma Proteomics
updated 23 months ago by 65k • written 23 months ago by • 0
2
votes
1
reply
1.7k
views
News: Announcing a short course in computational and statistical proteomics
proteomics massspectrometry R News
9.2 years ago vitek.olga ▴ 20
2
votes
1
reply
3.1k
views
Convert UniProt Entry Names into Gene Symbols
Proteomics ProteomicsWorkflow UniProt.ws
updated 3.2 years ago by 65k • written 3.2 years ago by ★ 1.5k
2
votes
0
replies
915
views
Job: PostDoc position for the analysis of large scale metabolomics data
metabolomics proteomics Job
3.6 years ago Johannes Rainer ★ 2.0k
2
votes
1
reply
1.2k
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
4.1 years ago harelarik ▴ 60
2
votes
5
replies
1.7k
views
NA coefficients values for samples with all zeros
limmagui proteomics
8.4 years ago vedran.franke • 0
2
votes
1
reply
945
views
Maximum parsimony protein assembly/inference
rforproteomics proteomics msnid msnbase
4.1 years ago daniel.magnus.bader ▴ 40
2
votes
3
replies
1.2k
views
rTANDEM package -- An R encapsulation of the X!Tandem algorithm
Proteomics rTANDEM Proteomics rTANDEM
updated 11.4 years ago by ★ 13k • written 11.4 years ago by ▴ 40
2
votes
1
reply
2.0k
views
DESeq package
Proteomics DESeq Proteomics DESeq
updated 11.5 years ago by ▴ 550 • written 11.5 years ago by ▴ 20
1
vote
3
replies
1.0k
views
Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
Limma proteomics limma
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
1
vote
2
replies
797
views
Errors installing "shinyTANDEM" package
software error proteomics
updated 5.1 years ago by 1.6k • written 5.1 years ago by • 0
1
vote
2
replies
2.0k
views
Errors installing mzR package
proteomics error
updated 5.1 years ago by 1.6k • written 5.1 years ago by • 0
1
vote
1
reply
1.0k
views
Define batch effect variables before removing them or getting rid of hidden surrogate variables
batch effect correction sva proteomics
5.4 years ago Sebastian Hesse ▴ 70
1
vote
1
reply
1.4k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.2 years ago by 1.6k
1
vote
2
replies
2.8k
views
Limma: technical and biological replicates in proteomics data
limma proteomics replicates
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
vote
6
replies
3.2k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 3.8 years ago by 1.6k • written 3.8 years ago by • 0
1
vote
3
replies
1.3k
views
Running GO analysis via Prostar
prostar proteomics rforproteomics annotationforge
updated 5.9 years ago by ▴ 10 • written 5.9 years ago by ▴ 20
1
vote
0
replies
1.6k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
5.2 years ago • updated 5.1 years ago Laurent Gatto 1.6k
1
vote
2
replies
1.8k
views
Proteomics: package/statistics to compare very different LFQ-proteomes
dep proteomics limma
4.3 years ago Rob • 0
1
vote
1
reply
2.0k
views
Job: junior level position in proteomics/data science
proteomics machine learning git docker Job
updated 6.3 years ago by • 0 • written 6.6 years ago by ▴ 70
1
vote
0
replies
1.9k
views
News: May Institute 2018 - Computation and statistics for mass spectrometry and proteomics at Northeastern University in Boston
bioconductor training course msstats proteomics News
6.3 years ago mnchoi67 ▴ 40
1
vote
1
reply
1.3k
views
Job: Post-doctoral mass spectrometry and proteomics bioinformatician (updated)
bioinformatics proteomics mass spectrometry job Job
6.9 years ago • updated 6.8 years ago Laurent Gatto 1.6k
1
vote
2
replies
1.5k
views
Deseq2 with replicate mean and variance information
deseq2 deseq differential analysis proteomics
6.1 years ago blehtine • 0
1
vote
1
reply
5.5k
views
Mfuzz: fill.NA - Warning messages: argument is not numeric or logical: returning NA
mfuzz clustering bioinformatics proteomics timecourse
updated 8.2 years ago by 1.6k • written 8.2 years ago by • 0
1
vote
8
replies
2.0k
views
DESEQ2 and continuous data
proteomics deseq2
8.2 years ago carandres74 • 0
50 results • Page 1 of 1
Recent ...
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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