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2
votes
4
replies
395
views
Should I exclude unmapped reads and proceed with the analysis for low mapped samples, or omit them altogether?
STAR mapping RNAseq
updated 10 weeks ago by ★ 1.9k • written 10 weeks ago by ▴ 60
0
votes
2
replies
484
views
Is there anything we can do when we have assignment rate below 50% in featurecounts?
RNA-seq featurecounts
updated 10 months ago by 43k • written 10 months ago by ▴ 60
0
votes
0
replies
358
views
How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific strandness RNAseq
10 months ago by Sib ▴ 60
1
vote
3
replies
744
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
10 months ago by Sib ▴ 60
2
votes
3
replies
884
views
Low mapping percentage
mapping STAR RNAseq
10 months ago by Sib ▴ 60
1
vote
2
replies
788
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
2.1k
views
How to understand logics and statistical concepts behind limma package?
R microarray DGE limma
updated 2.5 years ago by 141k • written 2.5 years ago by ▴ 60
0
votes
0
replies
508
views
Using machine learning methods to find a biomarker panel to diagnose a disease.
Machine-learning feature-selection training-dataset Biomarker RNAseq
2.6 years ago by Sib ▴ 60
0
votes
0
replies
867
views
Error in ReadAffy function
ReadAffy Microarray R
2.7 years ago by Sib ▴ 60
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 6 days ago by 43k • written 2.8 years ago by ▴ 60
0
votes
2
replies
810
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 6 days ago by 43k • written 2.9 years ago by ▴ 60
1
vote
11
replies
2.6k
views
Error in volcano plot drawing with R.
R
updated 3.5 years ago by ★ 7.0k • written 4.3 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
6.7k
views
How can I put the Rtools on PATH?
R
updated 3.9 years ago by 81k • 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
4.3 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
4.3 years ago by Sib ▴ 60
2
votes
4
replies
3.1k
views
Error in plotting Enhanced Volcano plot
differential expression analysis enhanced volcano
updated 4.3 years ago by ★ 5.8k • written 4.3 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
4.3 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 4.3 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 4.3 years ago by ▴ 140 • written 4.3 years ago by ▴ 60
2
votes
9
replies
4.5k
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
4.4k
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 ★ 5.8k • written 4.4 years ago by ▴ 60
5
votes
7
replies
5.6k
views
R does not put the chart in pdf
R
updated 4.4 years ago by 87k • written 4.4 years ago by ▴ 60
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