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Comment: C: Removing batch effects from microarray data based on only a subset of samples
6.9 years ago Ryan C. Thompson ★ 7.9k
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3.6k
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Answer: A: Applying SVA to RNA-Seq dataset
6.9 years ago Ryan C. Thompson ★ 7.9k
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2.0k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
6.9 years ago Ryan C. Thompson ★ 7.9k
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1
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1.8k
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Answer: A: Normalized counts after fitting linear model with batch effects - edgeR
6.9 years ago Ryan C. Thompson ★ 7.9k
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1.8k
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Comment: C: Normalized counts after fitting linear model with batch effects - edgeR
6.9 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.0k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
6.9 years ago Ryan C. Thompson ★ 7.9k
0
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1
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2.0k
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Comment: C: Help running the nondetects::qpcrImpute on my data?
6.9 years ago Ryan C. Thompson ★ 7.9k
0
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1
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7.8k
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Comment: C: Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
7.0 years ago Ryan C. Thompson ★ 7.9k
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1.5k
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Comment: C: DESeq2 Different Results when using different foreach parallel backends
7.0 years ago Ryan C. Thompson ★ 7.9k
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1.7k
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Comment: C: glmTreat Errors for multi coefficient and analysis of deviance situations.
7.0 years ago Ryan C. Thompson ★ 7.9k
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2
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1.7k
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Comment: C: glmTreat Errors for multi coefficient and analysis of deviance situations.
7.0 years ago Ryan C. Thompson ★ 7.9k
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1
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1.7k
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Answer: A: glmTreat Errors for multi coefficient and analysis of deviance situations.
7.0 years ago Ryan C. Thompson ★ 7.9k
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1
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1.7k
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Comment: C: normalization of CHIP-seq samples (ChIP and INPUT)
7.0 years ago Ryan C. Thompson ★ 7.9k
1
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1.9k
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Comment: C: Loads, really loads of DEGs after edgeR differential analysis
7.0 years ago Ryan C. Thompson ★ 7.9k
2
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1
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12k
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Comment: C: Effect of lfcThreshold on p-value in DESeq2
7.0 years ago Ryan C. Thompson ★ 7.9k
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1
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1.9k
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Answer: A: Loads, really loads of DEGs after edgeR differential analysis
7.0 years ago Ryan C. Thompson ★ 7.9k
1
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0
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5.2k
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Comment: C: Camera and ROAST
7.1 years ago Ryan C. Thompson ★ 7.9k
1
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0
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1.3k
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Answer: A: Mixed conditions: Design and contrast matrix
7.1 years ago Ryan C. Thompson ★ 7.9k
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0
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5.2k
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Comment: C: Camera and ROAST
7.1 years ago Ryan C. Thompson ★ 7.9k
1
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1
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864
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Answer: A: normalization of ChIP-seq
7.1 years ago Ryan C. Thompson ★ 7.9k
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8.4k
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Comment: C: Choosing a threshold for minimum counts in RNAseq
7.1 years ago Ryan C. Thompson ★ 7.9k
2
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2.0k
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
7.1 years ago Ryan C. Thompson ★ 7.9k
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1
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3.5k
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
7.1 years ago Ryan C. Thompson ★ 7.9k
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1
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1.1k
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Answer: A: Will large differences in the number of reads between samples decrease reliabili
7.1 years ago Ryan C. Thompson ★ 7.9k
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2.0k
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Comment: C: Is there are better way to improve the design via blocking or contrasts while us
7.1 years ago Ryan C. Thompson ★ 7.9k
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0
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1.2k
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Comment: C: Non-used samples changing number of significant genes in limma
7.2 years ago Ryan C. Thompson ★ 7.9k
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1
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1.2k
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Answer: A: Non-used samples changing number of significant genes in limma
7.2 years ago Ryan C. Thompson ★ 7.9k
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Comment: C: Limma: how to account for twin data (both MZ and DZ twins)?
7.2 years ago Ryan C. Thompson ★ 7.9k
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1.9k
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Can I meaningfully interpret a PCA or MDS plot of data with surrogate variable effects subtracted?
sva pca
updated 7.2 years ago by ▴ 120 • written 7.2 years ago by ★ 7.9k
0
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1
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12k
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Answer: A: Why different filtering criteria using CPM to filter the RNA-seq count data in e
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.8k
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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12k
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Comment: C: Why different filtering criteria using CPM to filter the RNA-seq count data in e
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.8k
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.8k
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Comment: C: When doing differential gene analysis, why measuring genes based on exons? Can w
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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1
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2.0k
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Answer: A: One-condition limma test
7.2 years ago Ryan C. Thompson ★ 7.9k
1
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1
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2.6k
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Answer: A: tximport recommendation for limma-trend downstream analysis?
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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0
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5.0k
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.2 years ago Ryan C. Thompson ★ 7.9k
1
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0
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1.8k
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Comment: C: EdgeR: Replicate samples diverge in MDS plot
7.2 years ago Ryan C. Thompson ★ 7.9k
2
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1
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1.8k
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Answer: A: EdgeR: Replicate samples diverge in MDS plot
7.2 years ago Ryan C. Thompson ★ 7.9k
1
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2
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5.0k
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Answer: A: Why limma, edgeR, and DESeq did not implement fold change moderation first?
7.2 years ago Ryan C. Thompson ★ 7.9k
3
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1
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2.4k
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Answer: A: limma-trend with random effects and/or array weights
7.2 years ago Ryan C. Thompson ★ 7.9k
0
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0
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1.3k
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Comment: C: Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
7.3 years ago Ryan C. Thompson ★ 7.9k
1
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2
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1.3k
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Can rtracklayer import tab-delimited BED files with unquoted spaces in fields?
rtracklayer bed software error
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ★ 7.9k
0
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0
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9.8k
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Comment: C: removeBatchEffect options: design and covariates
updated 7.3 years ago by 52k • written 10.4 years ago by ★ 7.9k
0
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1
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9.8k
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Comment: C: removeBatchEffect options: design and covariates
updated 7.3 years ago by 52k • written 10.4 years ago by ★ 7.9k
0
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0
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9.8k
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Comment: C: removeBatchEffect options: design and covariates
updated 7.3 years ago by 52k • written 10.4 years ago by ★ 7.9k
7
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3
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9.8k
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Answer: A: removeBatchEffect options: design and covariates
updated 7.3 years ago by 52k • written 10.4 years ago by ★ 7.9k
1
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0
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2.8k
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Comment: C: Why Differential expression results differ with edgeR and limma ?
7.3 years ago Ryan C. Thompson ★ 7.9k
0
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1
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1.5k
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Answer: A: Prefering Grouping variables or Interaction terms in Experimental Design
7.3 years ago Ryan C. Thompson ★ 7.9k
1
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1
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1.1k
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Comment: C: LFDR PROPTRUENULL LIMMA
7.4 years ago Ryan C. Thompson ★ 7.9k
819 results • Page 3 of 17
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