15
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23
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2.0k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 5 days ago Chris • 0
14
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17
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1.2k
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Why p value inconsistent when using different number of pathway score?
limma
15 days ago • updated 4 days ago Chris • 0
8
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7
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 hours ago by • 0 • written 6.7 years ago by ▴ 80
6
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19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 5 days ago by • 0 • written 4.6 years ago by ▴ 10
5
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6
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2.8k
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Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 3 days ago by 65k • written 2.3 years ago by • 0
3
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0
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69
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News: Bioconductor 3.19 is Released!
Release Bioconductor Packages Software
4 days ago shepherl 3.9k
3
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1
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472
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 8 hours ago by 50k • written 3 days ago by ▴ 10
3
votes
4
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204
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Help with error using camera() in limma
CAMERA limma
5 days ago Chris • 0
2
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2
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1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 5 days ago by • 0 • written 7.9 years ago by • 0
2
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3
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158
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
2
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2
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99
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fgsea significant result
fgsea
1 day ago • updated 18 hours ago Chris • 0
2
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2
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191
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 days ago Chris • 0
2
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3
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137
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package goseq seems to be not available on the latest version of R
goseq
updated 1 hour ago by 50k • written 2 days ago by ▴ 20
1
vote
1
reply
87
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Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by 41k • written 2 days ago by ▴ 10
1
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2
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325
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 2 days ago by 50k • written 2 days ago by • 0
1
vote
4
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479
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 4 days ago JKim • 0
1
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2
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176
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Improving the design matrices vignette in RNAseq123
RNAseq123
14 days ago • updated 39 minutes ago Lluís Revilla Sancho ▴ 730
1
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2
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296
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CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 2 days ago Kim • 0
1
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1
reply
106
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
1
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2
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66
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
12 hours ago • updated 13 minutes ago Chris • 0
0
votes
2
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97
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DESeq2 v1.35.0
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
votes
0
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43
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flowStats for CyTOF
flowStats
3 days ago tholmes • 0
0
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1
reply
97
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Gene-by-sample covariates in limma
Metabolomics limma
updated 3 days ago by 50k • written 3 days ago by • 0
0
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1
reply
102
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 3 days ago by 50k • written 3 days ago by • 0
0
votes
2
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130
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Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago kcarey • 0
0
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0
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124
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
11 days ago • updated 3 days ago glaciya2018 • 0
0
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2
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120
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
6 days ago • updated 3 days ago Aurora • 0
0
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0
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48
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dba.plotProfile() plotting and interpretation
DiffBind
2 days ago Henry ▴ 10
0
votes
0
replies
87
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Empty table plot using plotGseaTable()
fgsea
4 days ago • updated 2 days ago Chris • 0
0
votes
6
replies
201
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 2 days ago by ★ 1.3k • written 3 days ago by ▴ 130
0
votes
5
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2.8k
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DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.2 years ago • updated 15 hours ago Henrik Bengtsson ★ 2.4k
0
votes
29
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How to use bootRanges to bootstrap small RNA loci (nullranges package)
bootRanges nullranges
updated 15 hours ago by 41k • written 15 months ago by • 0
0
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2
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27
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Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 10 minutes ago by 6.7k • written 16 hours ago by • 0
0
votes
4
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245
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Minfi - estimatecellscount
min minfi
updated 6 days ago by 65k • written 5 weeks ago by • 0
0
votes
2
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31
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Couldn't connect to server while using "pathways"
DESeq2
updated just now by 41k • written 6 hours ago by • 0
0
votes
0
replies
72
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Could we detect difference at pathway level but not significant different at gene level?
GSVA
6 days ago Chris • 0
0
votes
1
reply
105
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putting my own expression data in deseq2
DESeq2
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
votes
1
reply
85
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Version 3.15 S4Vectors packages are missing
S4Vectors
updated 6 days ago by 3.9k • written 6 days ago by • 0
0
votes
0
replies
61
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
6 days ago Maria Doyle ▴ 70
0
votes
1
reply
101
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by 41k • written 6 days ago by • 0
0
votes
3
replies
166
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 5 days ago by ★ 1.9k • written 18 days ago by • 0
0
votes
3
replies
239
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 5 days ago by 65k • written 6 days ago by • 0
0
votes
1
reply
225
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots HMMcopy CopyNumberVariation
updated 5 days ago by 65k • written 6 days ago by • 0
0
votes
3
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1.5k
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Limma, eBayes different sample size of groups and adjustment
limma limma
updated 5 days ago by • 0 • written 13.0 years ago by ▴ 10
0
votes
3
replies
154
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Store output of matchPWM()
biostrings Biostrings
updated 4 days ago by 65k • written 4 days ago by ▴ 70
0
votes
1
reply
135
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
3
replies
247
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
votes
2
replies
222
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
5 days ago • updated 4 days ago Yveto • 0
0
votes
2
replies
165
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 13 days ago by • 0
0
votes
3
replies
132
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
54 results • Page 1 of 2
Recent ...
Replies
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
btw that was run on M1 mac
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Vincent J. Carey, Jr. 6.7k
the test is not portable > aa <- aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2") > str(aa) num [1:20, 1:20] 0.34 -0.0…
Comment: Method to find pathways different between 2 groups by Chris • 0
Sorry for not clear. I just try to find papers use this method for learning purpose. So I may know when to use this method. This paper comp…
Comment: Improving the design matrices vignette in RNAseq123 by Lluís Revilla Sancho ▴ 730
Cool. Thanks for looking into it.
Votes
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
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