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649
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Comment: Comment: Should I exclude unmapped reads and proceed with the analysis for low mapped sam
9 months ago by Sib ▴ 60
2
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4
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649
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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 months ago by ★ 2.5k • written 9 months ago by ▴ 60
0
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0
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606
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Comment: Comment: Is there anything we can do when we have assignment rate below 50% in featurecou
17 months ago by Sib ▴ 60
0
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2
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606
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Is there anything we can do when we have assignment rate below 50% in featurecounts?
RNA-seq featurecounts
updated 17 months ago by 44k • written 17 months ago by ▴ 60
0
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0
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439
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How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific strandness RNAseq
17 months ago by Sib ▴ 60
0
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1
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897
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Comment: Comment: What is the benefit of knowing the source of contamination when we have RNAseq d
18 months ago by Sib ▴ 60
1
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3
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897
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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
18 months ago by Sib ▴ 60
0
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0
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1.1k
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Comment: Comment: Low mapping percentage
18 months ago by Sib ▴ 60
2
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3
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1.1k
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Low mapping percentage
mapping STAR RNAseq
18 months ago by Sib ▴ 60
1
vote
2
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918
views
Why my application works well but when I try to modularize it, it doesn't work properly ?
Shinymodule app Shinyapp Shiny module
24 months ago by Sib ▴ 60
0
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0
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918
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Answer: Answer: Why my application works well but when I try to modularize it, it doesn't work p
24 months ago by Sib ▴ 60
6
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7
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2.8k
views
How to understand logics and statistical concepts behind limma package?
R microarray DGE limma
updated 3.1 years ago by 147k • written 3.1 years ago by ▴ 60
0
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0
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2.8k
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Answer: Answer: How to understand logics and statistical concepts behind limma package?
3.1 years ago by Sib ▴ 60
0
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2
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2.8k
views
Comment: Comment: How to understand logics and statistical concepts behind limma package?
3.1 years ago by Sib ▴ 60
0
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0
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597
views
Using machine learning methods to find a biomarker panel to diagnose a disease.
Machine-learning feature-selection training-dataset Biomarker RNAseq
3.2 years ago by Sib ▴ 60
0
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0
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983
views
Error in ReadAffy function
ReadAffy Microarray R
3.3 years ago by Sib ▴ 60
1
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0
replies
4.4k
views
Comment: Comment: Error in ComBat function: Error in dat[, batch == batch_level] : (subscript)
3.4 years ago by Sib ▴ 60
0
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1
reply
4.4k
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Comment: Comment: Error in ComBat function: Error in dat[, batch == batch_level] : (subscript)
3.4 years ago by Sib ▴ 60
3
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4
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4.4k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 7 months ago by 44k • written 3.4 years ago by ▴ 60
0
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0
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954
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Comment: Comment: Is it correct to merge two raw CEL datasets and then perform quality control, ba
3.4 years ago by Sib ▴ 60
0
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2
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954
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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 7 months ago by 44k • written 3.4 years ago by ▴ 60
1
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11
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3.0k
views
Error in volcano plot drawing with R.
R
updated 4.1 years ago by ★ 7.7k • written 4.9 years ago by ▴ 60
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1
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1.5k
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Comment: C: Can anyone introduce me a free tool for finding upstream regulators of different
4.2 years ago by Sib ▴ 60
4
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3
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1.5k
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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
4.2 years ago by Sib ▴ 60
0
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0
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7.0k
views
Comment: C: How can I put the Rtools on PATH?
4.5 years ago by Sib ▴ 60
0
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2
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7.0k
views
How can I put the Rtools on PATH?
R
updated 4.5 years ago by 85k • written 4.5 years ago by ▴ 60
0
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0
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1.4k
views
Comment: C: Is there a need for background correction and substitution of duplicates with th
4.9 years ago by Sib ▴ 60
0
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1
reply
1.4k
views
Comment: C: Is there a need for background correction and substitution of duplicates with th
4.9 years ago by Sib ▴ 60
0
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5
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1.4k
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
4.9 years ago by Sib ▴ 60
0
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1
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2.3k
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Comment: C: In R scripts of GEO2R which line is responsible for background correction and re
4.9 years ago by Sib ▴ 60
7
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5
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2.3k
views
In R scripts of GEO2R which line is responsible for background correction and replacing replicated probes with the mean?
R Differential expression analysis
4.9 years ago by Sib ▴ 60
0
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0
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3.4k
views
Comment: C: Error in plotting Enhanced Volcano plot
4.9 years ago by Sib ▴ 60
0
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1
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3.4k
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Comment: C: Error in plotting Enhanced Volcano plot
4.9 years ago by Sib ▴ 60
2
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4
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3.4k
views
Error in plotting Enhanced Volcano plot
differential expression analysis enhanced volcano
updated 4.9 years ago by ★ 6.9k • written 4.9 years ago by ▴ 60
0
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1
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3.0k
views
Comment: C: Error in volcano plot drawing with R.
4.9 years ago by Sib ▴ 60
0
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1
reply
3.0k
views
Comment: C: Error in volcano plot drawing with R.
4.9 years ago by Sib ▴ 60
0
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0
replies
3.0k
views
Comment: C: Error in volcano plot drawing with R.
4.9 years ago by Sib ▴ 60
0
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1
reply
3.0k
views
Comment: C: Error in volcano plot drawing with R.
4.9 years ago by Sib ▴ 60
0
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0
replies
1.4k
views
Comment: C: After differential expression analysis if we use gene symbols for further analys
4.9 years ago by Sib ▴ 60
0
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0
replies
1.2k
views
Comment: C: String db knows some gene symbols of DEGs for more than one protein and after e
4.9 years ago by Sib ▴ 60
3
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4
replies
1.4k
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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
4.9 years ago by Sib ▴ 60
0
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1
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1.4k
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Comment: C: After differential expression analysis if we use gene symbols for further analys
4.9 years ago by Sib ▴ 60
0
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1
reply
1.6k
views
Comment: C: Expression correlation tool
4.9 years ago by Sib ▴ 60
2
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2
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1.2k
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 4.9 years ago by ▴ 620 • written 4.9 years ago by ▴ 60
3
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1
reply
2.1k
views
Differentially expressed genes visualization with Cytoscape
Cytoscape PPI network visualization
updated 4.9 years ago by ▴ 140 • written 4.9 years ago by ▴ 60
0
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2
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5.3k
views
Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.9 years ago by Sib ▴ 60
0
votes
0
replies
5.3k
views
Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.9 years ago by Sib ▴ 60
0
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1
reply
5.3k
views
Comment: C: What this error means?Error in getEAWP(object) : data object isn't of a recogniz
4.9 years ago by Sib ▴ 60
2
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9
replies
5.3k
views
What this error means?Error in getEAWP(object) : data object isn't of a recognized data class
software error R
4.9 years ago by Sib ▴ 60
0
votes
0
replies
9.7k
views
Comment: C: How to prepare a input data for Cytoscape, genetic network software
5.0 years ago by Sib ▴ 60
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