Showing : DESeq2 • reset
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DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 10 hours ago by 33k • written 17 hours ago by • 0
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3
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62
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DESeq2: NA's in mcols(object)$betaConv
DESeq2
updated 10 hours ago by 33k • written 21 hours ago by • 0
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1
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27
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DESeq2: One or more designs for contrasts of interest
DESeq2
updated 22 hours ago by 33k • written 1 day ago by • 0
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2
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33
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
23 hours ago • updated 21 hours ago SUMIT • 0
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2
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46
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PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
1 day ago Clara • 0
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5
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72
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 1 day ago by 33k • written 1 day ago by ▴ 20
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4
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157
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matrix with Salmon gene-level quantifications in DESeq
DESeq2
updated 2 days ago by ▴ 640 • written 6 days ago by ▴ 10
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8
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216
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DESeq2: Variable Importance
DESeq2 RNASeq
updated 4 days ago by 33k • written 6 days ago by • 0
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1
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80
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DESeq2 - how to account for patient, batch and condition
DESeq2
updated 7 days ago by 57k • written 7 days ago by • 0
2
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3
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96
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RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 4 days ago by • 0 • written 8 days ago by • 0
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9
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202
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Why is my plot count does not fit with log fold change result?
DESeq2
updated 8 days ago by 33k • written 8 days ago by ▴ 30
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4
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99
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Number of genes differs between two design formulas in deseq2
DESeq2
9 days ago Mohamed Malek • 0
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6
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175
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Statistics on normalized counts
DESeq2
updated 8 days ago by • 0 • written 9 days ago by • 0
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3
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105
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[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 9 days ago by 33k • written 9 days ago by ▴ 10
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1
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83
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DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 9 days ago by 33k • written 12 days ago by • 0
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1
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83
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Why is the number of DEG different when comparing A versus B and B versus A?
DESeq2
updated 9 days ago by 33k • written 10 days ago by • 0
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2
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157
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where to download practice data
DESeq2
updated 13 days ago by ▴ 640 • written 14 days ago by • 0
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1
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80
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DESeq2: Paired samples (before and after treatment) with different responses
DESeq2
updated 13 days ago by ▴ 780 • written 13 days ago by • 0
2
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2
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125
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How to remove batch effect from multiple rna-seq dataset before running deseq2
DESeq2
13 days ago Yosapol • 0
0
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1
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98
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Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
14 days ago • updated 13 days ago Serge • 0
0
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3
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118
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Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 13 days ago by ▴ 780 • written 14 days ago by • 0
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1
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90
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[DESeq2] - Making DESeq Dataset object from csv of already normalized counts.
DESeq2
15 days ago Michael • 0
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2
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102
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DESeq2 - Cannot replicate log2FC calculations
DESeq2
15 days ago Sara • 0
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2
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108
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DESeq2 time-series with two conditions and several patients
DESeq2
17 days ago • updated 7 days ago Karolina Trachtova • 0
1
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2
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123
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Design Formula, PCA, and Sex Effect
DESeq2
18 days ago • updated 17 days ago GHI ▴ 10
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78
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DESeq2 "not full rank" with design design ~Gender+ Age
DESeq DESeq2
updated 19 days ago by ▴ 780 • written 19 days ago by • 0
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2
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5.6k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 2.4 years ago by ▴ 20
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5
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142
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Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 1 day ago by 33k • written 20 days ago by • 0
4
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3
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136
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Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 20 days ago by 33k • written 21 days ago by ▴ 30
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1
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68
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FDR Correction
dada2 Metagenomics DESeq2
updated 21 days ago by 33k • written 21 days ago by • 0
2
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8
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211
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
28 days ago • updated 20 days ago Jane • 0
6
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12
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256
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ColData use only certain variable within
DESeq2
22 days ago • updated 21 days ago Bine ▴ 10
0
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1
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77
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Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 22 days ago by 33k • written 23 days ago by • 0
1
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2
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124
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Plotting FPKM
ggplots2 DESeq2 fpkm()
22 days ago • updated 18 days ago Gime ▴ 10
1
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4
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116
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Incorrect 2-fold change reported in DESeq2 Data
DESeq2
23 days ago • updated 22 days ago Naphtap92 ▴ 10
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3
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88
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Can't install DESeq2 because of libxml
deseq2 libxml xml
updated 22 days ago by 33k • written 23 days ago by • 0
4
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14
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2.0k
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DESeq2 normalization vs VST vs rlog
deseq2
updated 25 days ago by 33k • written 22 months ago by • 0
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3
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130
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It takes a so long time to run DESeq2 on 1000 samples
DESeq2
updated 25 days ago by 33k • written 26 days ago by • 0
0
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1
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110
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DESeq2 design help
DESeq2
updated 27 days ago by 33k • written 27 days ago by • 0
0
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4
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115
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Inflation of zero or low counts in one condition - is DESeq2 with ZINB-WaVE an appropriate tool for such data?
DESeq2
27 days ago • updated 24 days ago miyakokodama • 0
0
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1
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95
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Multi-factor Analysis in DeSEQ2
tximport R tximportData RNASeq DESeq2
updated 27 days ago by 33k • written 27 days ago by • 0
2
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1
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127
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Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 28 days ago by 33k • written 4 weeks ago by • 0
1
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2
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108
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Different P-Adjusted Values In DESeq2 for the same comparaison
RNASeq DESeq2
29 days ago fernandogs97 • 0
0
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1
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94
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Dispersion Factors Not Being Calculated For Every Gene
DESeq2
updated 29 days ago by 33k • written 4 weeks ago by • 0
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4
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118
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
4 weeks ago jehimi • 0
0
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1
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94
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DESeq2 Design matrix
StatisticalMethod DESeq2
updated 4 weeks ago by 33k • written 4 weeks ago by • 0
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2
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115
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Technical reps
RNASeq DESeq2
updated 4 weeks ago by ▴ 640 • written 4 weeks ago by • 0
4
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7
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200
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Controlling for Batch Effect and Grouping in DESEQ2
DESeq2
updated 4 weeks ago by 33k • written 4 weeks ago by ▴ 10
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4
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274
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Problems installing DESeq2
DESeq2
4 weeks ago kvitt_silver • 0
1
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2
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110
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Grouping DESEQ2 with additional variable
DESeq2
4 weeks ago Bine ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Data input for aracne2regulon function in viper package by Luna_P • 0
Hello Keith, I am currently trying to use my ARACNE-AP generated networks in Viper. I did all three steps you mentioned above but my prob…
Answer: DESeq2 for allele-specific expression with contrasts between conditions by Michael Love 33k
There is a section in the vignette on interactions that will help you here. You want to test for within-individual effects (`allele`) and c…
Answer: Issues with Tximport by Michael Love 33k
Your file has no version numbers, while your `tx2gene` does have version numbers. While the names look similar, they are not a match. tximp…
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w by Michael Love 33k
This is fine and ignorable, it is coming from upstream packages: our use of a TxDb object to pull out transcript to gene mappings.
Comment: DESeq2: NA's in mcols(object)$betaConv by Michael Love 33k
They are actually rounded to zero in the `dds` which requires integer values.
Votes
Comment: DESeq2: NA's in mcols(object)$betaConv
Answer: Using tximeta::summarizeToGene function; Warning message: call dbDisconnect() w
simultaneous use of robust and weighting methods in limma
simultaneous use of robust and weighting methods in limma
Answer: RUVSeq and Salmon
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