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Comment: Comment: Preprocessing Issue
4.9 years ago Jeff Leek ▴ 650
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3.9k
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Comment: C: Which raw files (RNAseq) to download?
8.6 years ago Jeff Leek ▴ 650
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Answer: A: P value <0.05 and Q values~ 1
8.6 years ago Jeff Leek ▴ 650
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4.4k
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Answer: A: SVA behaving weirdly, system is computationally singular , problem with method
8.7 years ago Jeff Leek ▴ 650
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2.6k
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Comment: C: Using SVA with RRBS data
8.8 years ago Jeff Leek ▴ 650
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2.6k
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Answer: A: Using SVA with RRBS data
8.8 years ago Jeff Leek ▴ 650
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3.4k
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Answer: A: Handling both technical and biological replicates in Ballgown
8.8 years ago Jeff Leek ▴ 650
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2.3k
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Comment: C: Results with very few genes with qval <0.05
8.8 years ago Jeff Leek ▴ 650
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1
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1.7k
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Answer: A: IRanges error loading rsem data into ballgown
8.9 years ago Jeff Leek ▴ 650
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1
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4.7k
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Answer: A: The common error with ballgown has not been solved!
8.9 years ago Jeff Leek ▴ 650
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1
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1.4k
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Answer: A: Surrogate variables affecting just one sample?
9.0 years ago Jeff Leek ▴ 650
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1
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1.4k
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Answer: A: Surrogate variables affecting just one sample?
9.0 years ago Jeff Leek ▴ 650
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3.2k
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Comment: C: limma + voom + sva + complex RNA-seq design?
9.1 years ago Jeff Leek ▴ 650
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1
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2.5k
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Answer: A: Error in ball gown command
9.1 years ago Jeff Leek ▴ 650
1
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1.6k
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Answer: A: sva :: sva can variable of interest be a matrix itself?
9.1 years ago Jeff Leek ▴ 650
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3.8k
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Comment: C: SVA and proportion of variance explained
9.2 years ago Jeff Leek ▴ 650
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1
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3.8k
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Comment: C: SVA and proportion of variance explained
9.2 years ago Jeff Leek ▴ 650
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3.8k
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Answer: A: SVA and proportion of variance explained
9.2 years ago Jeff Leek ▴ 650
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2.2k
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Comment: C: I'm worried that I can't use "ballgown" well
9.2 years ago Jeff Leek ▴ 650
2
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4.7k
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Answer: A: about SVA: matrix of corrected expression values
9.3 years ago Jeff Leek ▴ 650
3
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1
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6.7k
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Answer: A: svaseq: how many and which surrogate variables to pick
9.3 years ago Jeff Leek ▴ 650
1
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2.2k
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Answer: A: Inspection of batch effect correction success with ComBat in R, regarding a merg
9.4 years ago Jeff Leek ▴ 650
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1
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1.8k
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Answer: A: Batch effect problem using SVA showing problems
9.4 years ago Jeff Leek ▴ 650
2
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1
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7.2k
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Answer: A: SVA: Error in svd((dats - rowMeans(dats))) : a dimension is zero
9.4 years ago Jeff Leek ▴ 650
2
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1
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1.4k
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Answer: A: Ballgown Custom Model Question
9.4 years ago Jeff Leek ▴ 650
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3.2k
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Comment: C: can we use sva function to estimate artifacts for rna seq data?
9.4 years ago Jeff Leek ▴ 650
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1
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3.2k
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Answer: A: can we use sva function to estimate artifacts for rna seq data?
9.4 years ago Jeff Leek ▴ 650
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1
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2.4k
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Comment: C: Ballgown from StringTie results transcripts which are not expressed in both cond
9.5 years ago Jeff Leek ▴ 650
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1
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2.4k
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Answer: A: Ballgown from StringTie results transcripts which are not expressed in both cond
9.5 years ago Jeff Leek ▴ 650
1
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1
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1.8k
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Answer: A: Polyester and mutations
9.5 years ago Jeff Leek ▴ 650
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955
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Answer: A: question for SVA package
9.6 years ago Jeff Leek ▴ 650
1
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2.4k
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Answer: A: Null model in SVA for patient paired test comparing tumor vs normal
9.6 years ago Jeff Leek ▴ 650
1
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2
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7.6k
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Comment: C: sva + egdeR - differential expression analysis - RNA-seq data
10.0 years ago Jeff Leek ▴ 650
2
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7.6k
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Answer: A: sva + egdeR - differential expression analysis - RNA-seq data
10.0 years ago Jeff Leek ▴ 650
3
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7.6k
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Answer: A: sva + egdeR - differential expression analysis - RNA-seq data
10.0 years ago Jeff Leek ▴ 650
0
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2.1k
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Answer: A: RMA and ComBat for 2 batches with samples in common
10.1 years ago Jeff Leek ▴ 650
0
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6.1k
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Answer: A: Running Combat in SVA with NA values in matrix
10.1 years ago Jeff Leek ▴ 650
1
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6.1k
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Answer: A: Running Combat in SVA with NA values in matrix
10.1 years ago Jeff Leek ▴ 650
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2.2k
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Answer: A: SomaticSignatures: negative entries after ComBat adjustment
10.1 years ago Jeff Leek ▴ 650
3
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2.5k
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Answer: A: Quantile normalization + sva for microarray experiment
10.1 years ago Jeff Leek ▴ 650
2
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12k
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Answer: A: Estimating and removing batch effects from rna-seq dataset
10.2 years ago Jeff Leek ▴ 650
1
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3.1k
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Answer: A: sva and svaseq for unsupervised analysis of expression data
10.3 years ago Jeff Leek ▴ 650
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2
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2.0k
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Answer: A: Reproducibility of results with ComBat
10.4 years ago Jeff Leek ▴ 650
0
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3.6k
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Answer: A: Use surrogate variables on DESeq2
10.4 years ago Jeff Leek ▴ 650
1
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0
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3.5k
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Answer: A: Problem with n.sv in sva package
10.4 years ago Jeff Leek ▴ 650
0
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1
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2.3k
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Answer: A: SVA package for RRBS - bisulfite methylation data
10.5 years ago Jeff Leek ▴ 650
1
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2.2k
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Answer: A: SVA batch effects for different technologies
10.6 years ago Jeff Leek ▴ 650
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3.1k
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Answer: A: Remove batch effect - condition partially confounded by data
11.0 years ago Jeff Leek ▴ 650
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3.1k
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Answer: A: Remove batch effect - condition partially confounded by data
11.0 years ago Jeff Leek ▴ 650
2
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1
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5.3k
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Answer: A: sva::ComBat without covariate of interest?
11.2 years ago Jeff Leek ▴ 650
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