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Comment: Comment: Should I exclude unmapped reads and proceed with the analysis for low mapped sam
9 weeks ago by Sib ▴ 60
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4
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392
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Should I exclude unmapped reads and proceed with the analysis for low mapped samples, or omit them altogether?
STAR mapping RNAseq
updated 9 weeks ago by ★ 1.9k • written 9 weeks ago by ▴ 60
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484
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Comment: Comment: Is there anything we can do when we have assignment rate below 50% in featurecou
10 months ago by Sib ▴ 60
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2
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484
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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
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0
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358
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How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific strandness RNAseq
10 months ago by Sib ▴ 60
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1
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742
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Comment: Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
10 months ago by Sib ▴ 60
1
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3
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742
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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
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0
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882
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Comment: Comment: Low mapping percentage
10 months ago by Sib ▴ 60
2
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3
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882
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Low mapping percentage
mapping STAR RNAseq
10 months ago by Sib ▴ 60
1
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2
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788
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Why my application works well but when I try to modularize it, it doesn't work properly ?
Shinymodule app Shinyapp Shiny module
16 months ago by Sib ▴ 60
0
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0
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788
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Answer: Answer: Why my application works well but when I try to modularize it, it doesn't work p
16 months ago by Sib ▴ 60
6
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7
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2.1k
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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
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0
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2.1k
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Answer: Answer: How to understand logics and statistical concepts behind limma package?
2.5 years ago by Sib ▴ 60
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2
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2.1k
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Comment: Comment: How to understand logics and statistical concepts behind limma package?
2.5 years ago by Sib ▴ 60
0
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0
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508
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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
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0
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867
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Error in ReadAffy function
ReadAffy Microarray R
2.7 years ago by Sib ▴ 60
1
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0
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3.8k
views
Comment: Comment: Error in ComBat function: Error in dat[, batch == batch_level] : (subscript)
2.8 years ago by Sib ▴ 60
0
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1
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3.8k
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Comment: Comment: Error in ComBat function: Error in dat[, batch == batch_level] : (subscript)
2.8 years ago by Sib ▴ 60
3
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4
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3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 3 days ago by 43k • written 2.8 years ago by ▴ 60
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0
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810
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Comment: Comment: Is it correct to merge two raw CEL datasets and then perform quality control, ba
2.8 years ago by Sib ▴ 60
0
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2
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810
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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 3 days ago by 43k • written 2.8 years ago by ▴ 60
1
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11
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2.6k
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Error in volcano plot drawing with R.
R
updated 3.5 years ago by ★ 7.0k • written 4.3 years ago by ▴ 60
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1
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1.2k
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Comment: C: Can anyone introduce me a free tool for finding upstream regulators of different
3.5 years ago by Sib ▴ 60
4
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3
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1.2k
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Can anyone introduce me a free tool for finding upstream regulators of differentially expressed genes?
upstream regulators enrichment analysis RNA-Seq
3.5 years ago by Sib ▴ 60
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0
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6.7k
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Comment: C: How can I put the Rtools on PATH?
3.9 years ago by Sib ▴ 60
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2
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6.7k
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How can I put the Rtools on PATH?
R
updated 3.9 years ago by 81k • written 3.9 years ago by ▴ 60
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0
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1.3k
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Comment: C: Is there a need for background correction and substitution of duplicates with th
4.3 years ago by Sib ▴ 60
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1
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1.3k
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Comment: C: Is there a need for background correction and substitution of duplicates with th
4.3 years ago by Sib ▴ 60
0
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5
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1.3k
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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
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1
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2.1k
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Comment: C: In R scripts of GEO2R which line is responsible for background correction and re
4.3 years ago by Sib ▴ 60
7
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5
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2.1k
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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
0
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0
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3.1k
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Comment: C: Error in plotting Enhanced Volcano plot
4.3 years ago by Sib ▴ 60
0
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1
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3.1k
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Comment: C: Error in plotting Enhanced Volcano plot
4.3 years ago by Sib ▴ 60
2
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4
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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
0
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1
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2.6k
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Comment: C: Error in volcano plot drawing with R.
4.3 years ago by Sib ▴ 60
0
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1
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2.6k
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Comment: C: Error in volcano plot drawing with R.
4.3 years ago by Sib ▴ 60
0
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0
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2.6k
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Comment: C: Error in volcano plot drawing with R.
4.3 years ago by Sib ▴ 60
0
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1
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2.6k
views
Comment: C: Error in volcano plot drawing with R.
4.3 years ago by Sib ▴ 60
0
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0
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1.3k
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Comment: C: After differential expression analysis if we use gene symbols for further analys
4.3 years ago by Sib ▴ 60
0
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0
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1.1k
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Comment: C: String db knows some gene symbols of DEGs for more than one protein and after e
4.3 years ago by Sib ▴ 60
3
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4
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1.3k
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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
0
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1
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1.3k
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Comment: C: After differential expression analysis if we use gene symbols for further analys
4.3 years ago by Sib ▴ 60
0
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1
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1.5k
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Comment: C: Expression correlation tool
4.3 years ago by Sib ▴ 60
2
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2
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1.1k
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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 4.3 years ago by ▴ 60
3
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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
0
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2
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4.5k
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Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.3 years ago by Sib ▴ 60
0
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0
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4.5k
views
Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.3 years ago by Sib ▴ 60
0
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1
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4.5k
views
Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.3 years ago by Sib ▴ 60
2
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9
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4.5k
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What this error means?Error in getEAWP(object) : data object isn't of a recognized data class
software error R
4.3 years ago by Sib ▴ 60
0
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0
replies
9.5k
views
Comment: C: How to prepare a input data for Cytoscape, genetic network software
4.4 years ago by Sib ▴ 60
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