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Overcoming confounding in batch effect correction
sva BiologicalQuestion
4 weeks ago • updated 29 days ago bbao ▴ 10
0
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2
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561
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
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3
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631
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Meta-analysis on RNA-seq data sets
meta-analysis sva Combat_Seq RNAseq
5 months ago Travis • 0
0
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4
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1.1k
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Generating surrogate variables across multiple variables of interest
sva
7 months ago Robert • 0
0
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3
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 11 months ago by ▴ 870 • written 11 months ago by • 0
3
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6
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1.1k
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
11 months ago nhaus ▴ 70
0
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2
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547
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
11 months ago michelafrancesconi8 • 0
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
11 months ago Lucy ▴ 60
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4
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 11 months ago by 43k • written 16 months ago by • 0
5
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9
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2.2k
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Batch correction and repeated measures
RUVSeq sva limma
updated 11 months ago by 52k • written 17 months ago by ▴ 10
4
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5
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12k
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[sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
sva
updated 7 months ago by • 0 • written 7.4 years ago by ▴ 60
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome by James W. MacDonald 68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column by Erika • 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping by James W. MacDonald 68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question? by DavideSant • 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data by silickas • 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
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Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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