Showing : Proteomics • reset
0
votes
16
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1.3k
views
liimma and Across Array Normalisation
Microarray Proteomics Microarray Proteomics
updated 8.5 years ago by 46k • written 8.5 years ago by ▴ 130
1
vote
12
replies
9.8k
views
Using limma for quantitative proteomics data
Microarray Proteomics limma Microarray Proteomics limma
10.2 years ago • updated 10.1 years ago Yong Li ▴ 80
2
votes
12
replies
948
views
msmsTests, NA values in test.results output
Proteomics msmstests FDR
updated 3.8 years ago by 1.5k • written 3.8 years ago by • 0
0
votes
10
replies
795
views
warning in lumi
Proteomics lumi Proteomics lumi
updated 10.5 years ago by 25k • written 10.5 years ago by ▴ 110
1
vote
9
replies
1.7k
views
msnbase error when adding identification data
msnbase proteomics itraq
updated 7.6 years ago by 1.5k • written 7.6 years ago by • 0
0
votes
9
replies
1.1k
views
RforProteomics workflow troubleshooting
proteomics
6.1 years ago yockpingchow • 0
25
votes
9
replies
5.1k
views
voom for spectral counts
limma voom proteomics spectral counts massspectrometry
updated 7.5 years ago by 46k • written 7.5 years ago by ▴ 40
4
votes
9
replies
1.3k
views
Limma is doing the right way to calculate the fold change?
limma proteomics
updated 5.2 years ago by 1.5k • written 5.2 years ago by ▴ 30
0
votes
8
replies
1.3k
views
IPI to entrez id
Proteomics GO biomaRt Proteomics GO biomaRt
11.4 years ago Dick Beyer ★ 1.4k
0
votes
8
replies
925
views
Bimodal Distrinbution
Proteomics Proteomics
updated 13.7 years ago by ▴ 120 • written 13.7 years ago by ▴ 20
0
votes
8
replies
1.7k
views
Getting data into (and out of) the MSnSet object
proteomics MSnbase MSnSet readMSnSet msmsTests
updated 3.0 years ago by • 0 • written 4.6 years ago by ▴ 20
1
vote
8
replies
1.4k
views
DESEQ2 and continuous data
proteomics deseq2
6.5 years ago carandres74 • 0
0
votes
7
replies
867
views
getBioC and install.packages2 fail
Proteomics reposTools Proteomics reposTools
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 210
2
votes
7
replies
984
views
I get nothing in my up and down regulated genes
limma proteomics label free
6.0 years ago Nemo ▴ 80
1
vote
6
replies
1.5k
views
DEP package: Problems installing on macOS
software error DEP proteomics
updated 2.1 years ago by 1.5k • written 2.1 years ago by • 0
5
votes
6
replies
734
views
possible package naming conflict
proteomics
20 months ago Tobias ▴ 30
6
votes
6
replies
739
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 17 months ago by 46k • written 17 months ago by ▴ 10
0
votes
5
replies
1.6k
views
Package plgem for analysis of spectral counts, was 'limma for spectral counts'
Microarray Proteomics limma plgem Microarray Proteomics limma plgem
updated 11.8 years ago by ▴ 120 • written 11.8 years ago by ▴ 70
2
votes
5
replies
260
views
proteomics analysis
Proteomics analysis
updated 4 weeks ago by ▴ 70 • written 4 weeks ago by • 0
2
votes
5
replies
1.1k
views
NA coefficients values for samples with all zeros
limmagui proteomics
6.7 years ago vedran.franke • 0
0
votes
5
replies
714
views
Error loading charm
Proteomics Proteomics
updated 10.3 years ago by ★ 4.3k • written 10.3 years ago by ▴ 110
4
votes
5
replies
1.1k
views
How to convert a xlsx data file to MSnSet format?
msnbase msmstests proteomics lc-ms/ms msnID
updated 3.5 years ago by 1.5k • written 3.5 years ago by ▴ 10
0
votes
5
replies
815
views
Trouble using addMarkers from pRoloc on my own dataset
proloc proteomics msnset
4.5 years ago moldach ▴ 20
0
votes
5
replies
390
views
In need of linear modeling help for differential expression (proteomics)
Proteomics limma vsn
updated 11 months ago by 46k • written 11 months ago by • 0
1
vote
5
replies
1.8k
views
Using Limma for proteomics (2D DIGE) datasets
Proteomics limma impute limmaGUI Proteomics limma impute limmaGUI
updated 7.1 years ago by • 0 • written 12.8 years ago by ▴ 60
1
vote
4
replies
720
views
Adding annotation to MSnSet
bioconductor proteomics msnset
updated 4.4 years ago by 1.5k • written 4.4 years ago by ▴ 20
0
votes
4
replies
431
views
DEP - Run filter_missval() with a threshold ranging from 0 to 3
proteomics DEP
17 months ago rina ▴ 20
0
votes
4
replies
968
views
Cannot install and load MSstats package
proteomics massspectrometry msstats
updated 4.4 years ago by 1.5k • written 4.4 years ago by • 0
0
votes
4
replies
816
views
Query about the conditional hypergeometric test in GOstats package
Proteomics Proteomics
updated 14.7 years ago by 60k • written 14.7 years ago by ▴ 130
3
votes
4
replies
1.1k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 4.8 years ago by ▴ 150 • written 4.8 years ago by ▴ 10
2
votes
4
replies
942
views
how to find up regulated proteins from a label free
deseq2 proteomics label free
updated 6.0 years ago by 1.5k • written 6.0 years ago by ▴ 80
0
votes
4
replies
845
views
Bioconductor Digest, Vol 84, Issue 19
Proteomics Proteomics
updated 12.5 years ago by 25k • written 12.5 years ago by ★ 1.4k
3
votes
4
replies
805
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 3.8 years ago by ▴ 80 • written 3.8 years ago by • 0
0
votes
4
replies
405
views
How to analyse RNA-based protein pulldown mass spectrometry data
Proteomics limma MassSpectrometry
13 months ago barrypraveen • 0
0
votes
3
replies
629
views
Find DEPs among TMT labeling proteom time course data by limma
limma proteomics TMTlabeling timecoursedata
updated 21 months ago by ▴ 270 • written 21 months ago by • 0
1
vote
3
replies
795
views
a good pipline for proteomics
proteomics r
updated 6.9 years ago by 1.5k • written 6.9 years ago by ▴ 80
0
votes
3
replies
730
views
Using CDF file on affylmGUI
Proteomics GO affylmGUI Proteomics GO affylmGUI
updated 15.7 years ago by ▴ 450 • written 15.7 years ago by ▴ 70
0
votes
3
replies
442
views
Why I can not install rTANDEM?
MassSpectrometry Proteomics mzR
20 months ago Gilad • 0
0
votes
3
replies
717
views
multtest error - class label problem
Proteomics Proteomics
updated 16.1 years ago by ▴ 10 • written 16.2 years ago by ▴ 20
0
votes
3
replies
1.8k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
14.1 years ago anna freni sterrantino ▴ 120
0
votes
3
replies
1.4k
views
limma and Volcano Plots
Microarray Proteomics Cancer PROcess Microarray Proteomics Cancer PROcess
updated 8.5 years ago by 46k • written 8.5 years ago by ▴ 130
1
vote
3
replies
1.2k
views
Isobar - generating IBSpectra object
isobar mzid mgf proteomics itraq
updated 7.6 years ago by 1.5k • written 7.6 years ago by • 0
5
votes
3
replies
1.1k
views
Strong upwards correlation between log fold change and average log expression in MD plot of Limma
limma proteomics
updated 4.8 years ago by 46k • written 4.8 years ago by • 0
2
votes
3
replies
883
views
rTANDEM package -- An R encapsulation of the X!Tandem algorithm
Proteomics rTANDEM Proteomics rTANDEM
updated 9.6 years ago by 13k • written 9.6 years ago by ▴ 40
1
vote
3
replies
560
views
Interpreting Fold Change Calculation in Limma to Non-Statisticians: Sanity Check
Limma proteomics limma
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
0
votes
3
replies
1.2k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 14.5 years ago by 25k • written 14.5 years ago by ▴ 70
0
votes
3
replies
476
views
What does component or SCX classification in iTRAQ/TMT experiment represent?
proteomics
updated 3.7 years ago by 1.5k • written 3.7 years ago by • 0
3
votes
3
replies
592
views
Clarification of results tables in DEP
DEP proteomics
updated 3.0 years ago by ▴ 70 • written 3.1 years ago by ▴ 490
0
votes
3
replies
2.5k
views
from RefSeq to GO terms / gene symbol to geneID
Proteomics Coverage Annotation GO Proteomics Coverage Annotation GO
15.2 years ago • updated 15.1 years ago Simon Lin ▴ 270
0
votes
3
replies
718
views
PCA or concordance
Proteomics Proteomics
updated 12.4 years ago by 21k • written 12.4 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: I cannot install "microbiome" by Marcel Ramos 570
Hi @61191329 , Unfortunately, I am unable to reproduce the issue on Windows. Please provide additional information, namely `BiocManager::v…
Comment: DESeq2 LFC changes sign after adjusting for surrogates by Marie • 0
Thanks a lot!
Comment: how to use Rsamtools to parse extra fields from STAR alignment by Jiping Wang ▴ 90
Thanks so much! That's exactly the solution I am looking for.
Comment: Mapping genome regions to gene symbols by michaelwegert • 0
function > elementLengths() was deprecated in S4Vectors version update 0.16.0 (in 2016?). \ So I used: > elementNROWS() [https://web.m…
Comment: OPLS-DA: confidence interval for accuracy metric by etienne.thevenot ▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Votes
A: log2FoldChange calculation in DESeq2 output
A: DESeq2 baseMean counts
Answer: error running UniProt.ws
error running UniProt.ws
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
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