2
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5
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
4 hours ago • updated 57 minutes ago Alexandre • 0
2
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5
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125
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 58 minutes ago by 65k • written 1 day ago by • 0
0
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1
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43
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PCA plot suggestions
DESeq2 PCAtools
updated 3 hours ago by • 0 • written 13 hours ago by • 0
0
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3
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109
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 4 hours ago by 65k • written 1 day ago by • 0
0
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0
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One error problem occurred caused by data type during using GDCprepare to handle BRCA data
GDCRNATools TCGA
9 hours ago glaciya2018 • 0
1
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
1 day ago • updated 9 hours ago ATpoint ★ 4.0k
0
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2
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featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_get_next_read_BIN: Assertion `l_name < 256' failed. Aborted (core dumpe…
metaMSdata
2 days ago • updated 11 hours ago shuwangxinze1996 • 0
0
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8
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 11 hours ago by ★ 1.3k • written 2 days ago by • 0
0
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1
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 hours ago by 41k • written 23 hours ago by • 0
1
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13
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253
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
3 days ago • updated 20 hours ago fernanda.backsouza ▴ 10
10 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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?
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