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updated 1 day ago by 41k • written 1 day ago by • 0
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limma Intercept vs No-intercept models completely changing DMR results?
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updated 3 days ago by • 0 • written 4.6 years ago by ▴ 10
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Why p value inconsistent when using different number of pathway score?
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13 days ago • updated 2 days ago Chris • 0
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Padj "NA" with thousands of low count although the raw read counts are quite large
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updated 3 days ago by ★ 1.9k • written 15 days ago by • 0
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5 weeks ago • updated 3 days ago Chris • 0
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updated 3 days ago by 65k • written 4 days ago by • 0
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212
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How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
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3 days ago Chris • 0
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10 weeks ago • updated 2 days ago JKim • 0
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updated 2 days ago by 65k • written 2 days ago by ▴ 70
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NEED FOR NESSASORY HELP
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4 days ago Chris • 0
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log2FoldChange value is way too different when compared with counts(dds)
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updated 2 days ago by 41k • written 3 days ago by • 0
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2 days ago • updated 1 day ago Ian D. ▴ 70
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updated 1 day ago by 65k • written 2.3 years ago by • 0
0
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71
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Gene-by-sample covariates in limma
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updated 1 day ago by 50k • written 1 day ago by • 0
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Deseq2 and Normalization of RNA sequencing data
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3 days ago • updated 17 hours ago Aurora • 0
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updated 14 hours ago by 65k • written 1 day ago by ▴ 130
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updated 8 hours ago by 41k • written 8 hours ago by • 0
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CombineArrays for EPIC and EPIC V2
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4 weeks ago • updated 6 hours ago Kim • 0
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updated 3 hours ago by 50k • written 7 hours ago by • 0
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1
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114
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
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2 days ago shepherl 3.9k
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Could we detect difference at pathway level but not significant different at gene level?
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4 days ago Chris • 0
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how to do Differential splicing from SGSeq analysis
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9 days ago • updated 4 days ago Sara • 0
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9 hours ago Henry ▴ 10
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0
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22
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Handling multiple differential expression comparisons
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9 hours ago Zainab • 0
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3
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108
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Differences in differential analysis methods for RNA-Seq
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updated 1 day ago by ★ 4.1k • written 2 days ago by • 0
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Job: Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 1 day ago by • 0
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One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
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8 days ago • updated 18 hours ago glaciya2018 • 0
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How to create consensus peak sets for each group to use in DiffBind?
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DiffBind: no peaks in DBA object
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1 day ago yvonneh • 0
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Empty table plot using plotGseaTable()
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2 days ago • updated 6 hours ago Chris • 0
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3 days ago Maria Doyle ▴ 70
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flowStats for CyTOF
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1 day ago tholmes • 0
49 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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