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2
votes
4
replies
432
views
Should I exclude unmapped reads and proceed with the analysis for low mapped samples, or omit them altogether?
STAR mapping RNAseq
updated 3 months ago by ★ 2.0k • written 3 months ago by ▴ 60
0
votes
2
replies
507
views
Is there anything we can do when we have assignment rate below 50% in featurecounts?
RNA-seq featurecounts
updated 11 months ago by 43k • written 11 months ago by ▴ 60
0
votes
0
replies
367
views
How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific strandness RNAseq
11 months ago by Sib ▴ 60
1
vote
3
replies
764
views
What is the benefit of knowing the source of contamination when we have RNAseq data with less than 70% mapping?
alignment mapping STAR contamination RNAseq
11 months ago by Sib ▴ 60
2
votes
3
replies
914
views
Low mapping percentage
mapping STAR RNAseq
11 months ago by Sib ▴ 60
1
vote
2
replies
805
views
Why my application works well but when I try to modularize it, it doesn't work properly ?
Shinymodule app Shinyapp Shiny module
17 months ago by Sib ▴ 60
6
votes
7
replies
2.2k
views
How to understand logics and statistical concepts behind limma package?
R microarray DGE limma
updated 2.6 years ago by 142k • written 2.6 years ago by ▴ 60
0
votes
0
replies
523
views
Using machine learning methods to find a biomarker panel to diagnose a disease.
Machine-learning feature-selection training-dataset Biomarker RNAseq
2.7 years ago by Sib ▴ 60
0
votes
0
replies
883
views
Error in ReadAffy function
ReadAffy Microarray R
2.8 years ago by Sib ▴ 60
3
votes
4
replies
3.9k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 4 weeks ago by 43k • written 2.9 years ago by ▴ 60
0
votes
2
replies
834
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R microarray affymetrix batch-effect quality-control
updated 4 weeks ago by 43k • written 2.9 years ago by ▴ 60
1
vote
11
replies
2.7k
views
Error in volcano plot drawing with R.
R
updated 3.6 years ago by ★ 7.2k • written 4.4 years ago by ▴ 60
4
votes
3
replies
1.3k
views
Can anyone introduce me a free tool for finding upstream regulators of differentially expressed genes?
upstream regulators enrichment analysis RNA-Seq
3.6 years ago by Sib ▴ 60
0
votes
2
replies
6.8k
views
How can I put the Rtools on PATH?
R
updated 3.9 years ago by 82k • written 3.9 years ago by ▴ 60
0
votes
5
replies
1.3k
views
Is there a need for background correction and substitution of duplicates with the mean when we use the getGEO function of R in microarray analysis?
R GEO Microarray analysis
4.4 years ago by Sib ▴ 60
7
votes
5
replies
2.1k
views
In R scripts of GEO2R which line is responsible for background correction and replacing replicated probes with the mean?
R Differential expression analysis
4.4 years ago by Sib ▴ 60
2
votes
4
replies
3.2k
views
Error in plotting Enhanced Volcano plot
differential expression analysis enhanced volcano
updated 4.4 years ago by ★ 6.0k • written 4.4 years ago by ▴ 60
3
votes
4
replies
1.3k
views
After differential expression analysis if we use gene symbols for further analysis we lose some DEGs. Is it ok?
Differential expression analysis GEO
4.4 years ago by Sib ▴ 60
2
votes
2
replies
1.1k
views
String db knows some gene symbols of DEGs for more than one protein and after entering gene symbols ask to select the desiered gene.
R Cytoscape String app network visualization
updated 4.4 years ago by ▴ 620 • written 4.4 years ago by ▴ 60
3
votes
1
reply
2.0k
views
Differentially expressed genes visualization with Cytoscape
Cytoscape PPI network visualization
updated 4.4 years ago by ▴ 140 • written 4.4 years ago by ▴ 60
2
votes
9
replies
4.7k
views
What this error means?Error in getEAWP(object) : data object isn't of a recognized data class
software error R
4.4 years ago by Sib ▴ 60
1
vote
2
replies
1.1k
views
which ID of differentially expressed genes from the result page of the GEO2R is used to the construction of the Protein-Protein interaction network i…
gene
4.4 years ago by Sib ▴ 60
3
votes
6
replies
4.5k
views
How to obtain gene symbols from the result list of GEO2R?
rna-seq R
updated 4.4 years ago by ▴ 70 • written 4.4 years ago by ▴ 60
7
votes
6
replies
2.0k
views
Are gene symbol and HGNC symbol the same names for a gene?
gene RNA-Seq
updated 4.4 years ago by ★ 6.0k • written 4.4 years ago by ▴ 60
5
votes
7
replies
5.7k
views
R does not put the chart in pdf
R
updated 4.4 years ago by 88k • written 4.4 years ago by ▴ 60
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