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Answer: Answer: suprisingly high logFC using limma
13 months ago by Gordon Smyth ★ 7.2k
3
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1
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1.5k
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Answer: Answer: extract gene coordinates and TSS from gene list
13 months ago by Gordon Smyth ★ 7.2k
1
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1
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1.5k
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Answer: Answer: How to remove unknown batch-batch effects from GEO datasets
13 months ago by Gordon Smyth ★ 7.2k
4
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1
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4.8k
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Answer: Answer: Get TPM from RNA counts and gene length?
15 months ago by Gordon Smyth ★ 7.2k
0
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0
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604
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Answer: Answer: How to decide the best threshold for filtering probes in limma
15 months ago by Gordon Smyth ★ 7.2k
1
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0
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579
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Answer: Answer: How should I interpret FB_Plot in microarray analysis?
15 months ago by Gordon Smyth ★ 7.2k
3
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0
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1.1k
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Answer: Answer: How should I deduce the variable from its variance and expectation in the `voom`
15 months ago by Gordon Smyth ★ 7.2k
0
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1
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2.1k
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Answer: Answer: Limma for batch effect correction
15 months ago by Gordon Smyth ★ 7.2k
0
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0
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680
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Answer: Answer: interpreting voom mean variance plots with large BCV and faint kink
15 months ago by Gordon Smyth ★ 7.2k
0
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1
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720
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Answer: Answer: finding error to run edgeR, error in ploting MDS and after that in model matrix
15 months ago by Gordon Smyth ★ 7.2k
6
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0
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2.2k
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Answer: Answer: Hugely different results between edgeR and DESeq2
15 months ago by Gordon Smyth ★ 7.2k
2
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0
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1.0k
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Answer: Answer: Processed RNA seq data publicly available
16 months ago by Gordon Smyth ★ 7.2k
3
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0
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1.6k
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Answer: Answer: R is assigning unique identifier to the same column names when reading in as a d
16 months ago by Gordon Smyth ★ 7.2k
1
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0
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1.8k
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Answer: Answer: R programmin RNA seq
16 months ago by Gordon Smyth ★ 7.2k
4
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1
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1.9k
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Answer: Answer: How to make contrasts to find genes DE in one experimental group but NOT in othe
16 months ago by Gordon Smyth ★ 7.2k
2
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0
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1.1k
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Answer: Answer: Strange results from limma output
17 months ago by Gordon Smyth ★ 7.2k
1
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1
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1.2k
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Answer: Answer: Accounting for differential abundance in differential expression in scRNAseq
17 months ago by Gordon Smyth ★ 7.2k
0
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1
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1.4k
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Answer: Answer: How to remove duplicate rows by averaging their values having 1 million rows X 1
17 months ago by Gordon Smyth ★ 7.2k
5
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1
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2.5k
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Answer: Answer: Different featureCounts data using GTF annotation file from two different source
17 months ago by Gordon Smyth ★ 7.2k
1
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0
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483
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Answer: Answer: microarray differential expression analyses
18 months ago by Gordon Smyth ★ 7.2k
2
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1
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2.5k
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Answer: Answer: Error input data must be numeric in R, how to solve it?
18 months ago by Gordon Smyth ★ 7.2k
0
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1
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1.6k
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Answer: Answer: Filtering bad quality probes in illumina microarray data
18 months ago by Gordon Smyth ★ 7.2k
1
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0
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961
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Answer: Answer: is normalize RNA seq raw counts used correctly?
18 months ago by Gordon Smyth ★ 7.2k
0
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0
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1.2k
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Answer: Answer: Can I run EdgeR or DESeq2 on bimodal data caused by batch effect?
18 months ago by Gordon Smyth ★ 7.2k
2
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1
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1.4k
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Answer: Answer: Question about edgeR GLM funcionality
18 months ago by Gordon Smyth ★ 7.2k
1
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0
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519
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Answer: Answer: EdgeR: apply minimum cpm threshold only to certain samples
19 months ago by Gordon Smyth ★ 7.2k
0
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0
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1.3k
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Answer: Answer: How to perform paired t-test in R for obtaining p-value of each gene?
19 months ago by Gordon Smyth ★ 7.2k
0
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1
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1.2k
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Answer: Answer: How to apply two tailed paired t-test in limma for DEGs selection?
19 months ago by Gordon Smyth ★ 7.2k
0
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0
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995
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Answer: Answer: HELP- analysis RNa-seq from GEO
19 months ago by Gordon Smyth ★ 7.2k
1
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1
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733
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Answer: Answer: Microarray DEG analysis visualisation
19 months ago by Gordon Smyth ★ 7.2k
1
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0
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932
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Answer: Answer: Reads mapping to pseudogenes using RSubread
19 months ago by Gordon Smyth ★ 7.2k
1
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0
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1.1k
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Answer: Answer: Create the design matrix for limma differential expression analysis.
19 months ago by Gordon Smyth ★ 7.2k
1
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1
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1.5k
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Answer: Answer: EDAseq, edgeR libraries cannot be installed in M2 mac
19 months ago by Gordon Smyth ★ 7.2k
4
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1
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1.5k
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Answer: Answer: Same results in Limma Toptable as in DESEQ2 results
20 months ago by Gordon Smyth ★ 7.2k
1
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1
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2.6k
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Answer: Answer: Limma Differential Expression contrast matrix with several variables
20 months ago by Gordon Smyth ★ 7.2k
3
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1
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1.4k
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Answer: Answer: Obtaining p-value and fold-change from a table
21 months ago by Gordon Smyth ★ 7.2k
2
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1
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795
views
Answer: Answer: When is the correct timing to perform edgeR cpm calculation?
21 months ago by Gordon Smyth ★ 7.2k
3
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0
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1.2k
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Answer: Answer: scRNA-seq: depositing count matrix without providing raw data
22 months ago by Gordon Smyth ★ 7.2k
1
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0
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921
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Answer: Answer: Include DEGs with a -l2fc in overrepresentation analysis?
22 months ago by Gordon Smyth ★ 7.2k
1
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0
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1.1k
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Answer: Answer: load csv file to edgeR
22 months ago by Gordon Smyth ★ 7.2k
2
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1
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2.9k
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Answer: Answer: File not in gzip format
22 months ago by Gordon Smyth ★ 7.2k
4
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1
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2.1k
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Answer: Answer: [R] How to make Contrast for Differential Expressed with more classes than 2
23 months ago by Gordon Smyth ★ 7.2k
1
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1
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982
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Answer: Answer: comparing fragmented RNA-seq to non-fragmented RNA-seq
23 months ago by Gordon Smyth ★ 7.2k
1
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1
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1.2k
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Answer: Answer: limma voom -- all genes after filtering are differentially expressed
23 months ago by Gordon Smyth ★ 7.2k
4
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2
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870
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Answer: Answer: Error when using edgeR with only two samples
23 months ago by Gordon Smyth ★ 7.2k
1
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0
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549
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Answer: Answer: exact counts tables for limma voom guide
23 months ago by Gordon Smyth ★ 7.2k
1
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0
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961
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Answer: Answer: Limma voom with missing values from mass spectrometry
23 months ago by Gordon Smyth ★ 7.2k
0
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1
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1.4k
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Answer: Answer: Limma for paired and unpaired samples. Strange number of DEGs in unpaired sample
24 months ago by Gordon Smyth ★ 7.2k
5
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3
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3.4k
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Answer: Answer: How to regress out age and sex using limma removeBatchEffect
24 months ago by Gordon Smyth ★ 7.2k
0
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0
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1.8k
views
Answer: Answer: How to choose threshold for filtering low counts before Voom transformation?
2.0 years ago by Gordon Smyth ★ 7.2k
288 results • Page 2 of 6
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