Showing : ebseq • reset
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DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
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EBSeq-HMM: retrieving expression paths for genes differing by time AND treatment
ebseq ebseq-hmm rna-seq
8.5 years ago vieuphoria ▴ 10
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TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by ▴ 100
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DE analysis with reference transcriptome
Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 10
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EBSeq package gives NaN Values for EBMultiTest
differential expression ebseq rnaseq
9.0 years ago jbarker2 • 0
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1.4k
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How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
8.8 years ago jackipchiho ▴ 10
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Matching New Samples to Differential Expression Profile
differential expression ebseq rnaseq
8.8 years ago jbarker2 • 0
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[EBSeq] Normalization and DE genes detection
ebseq normalization differential gene expression
7.9 years ago jean.keller ▴ 10
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920
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[EBSEQ] Strange NA values
ebseq differential gene expression
7.8 years ago jean.keller ▴ 10
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3
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888
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Heatmap for ebseq2 output
ebseq
4.9 years ago drkousi31 • 0
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1.6k
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by 50k
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560
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EBTest error please add gene/isoform names to the data matrix
EBSeq
3.9 years ago lli2 • 0
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1.0k
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EBSeq Results Affected By Outlying Values
EBSeq EBSeq
10.3 years ago Dario Strbenac ★ 1.5k
13 results • Page 1 of 1
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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Votes
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
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