2
votes
2
replies
66
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 hours ago by 41k • written 3 hours ago by • 0
1
vote
2
replies
253
views
CombineArrays for EPIC and EPIC V2
EPICV1 Methylation combineArrays minifi EPICv2manifest
4 weeks ago • updated 1 hour ago Kim • 0
0
votes
2
replies
99
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 22 hours ago kcarey • 0
0
votes
1
reply
160
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 18 hours ago by 50k • written 1 day ago by ▴ 10
0
votes
0
replies
93
views
One error problem occurred caused by data type during using GDCprepare function of TCGAbiolinks to handle TCGAbiolinks BRCA data
GDCRNATools TCGA
8 days ago • updated 13 hours ago glaciya2018 • 0
0
votes
2
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103
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 12 hours ago Aurora • 0
0
votes
5
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121
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 hours ago by 65k • written 1 day ago by ▴ 130
0
votes
0
replies
15
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dba.plotProfile() plotting and interpretation
DiffBind
5 hours ago • updated 4 hours ago Henry ▴ 10
0
votes
0
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17
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Handling multiple differential expression comparisons
DESeq2
4 hours ago Zainab • 0
0
votes
0
replies
13
views
package goseq seems to be not available on the latest version of R
goseq
2 hours ago Patrycja • 0
0
votes
0
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66
views
Empty table plot using plotGseaTable()
fgsea
2 days ago • updated 1 hour ago Chris • 0
0
votes
1
reply
69
views
Gene-by-sample covariates in limma
Metabolomics limma
updated 23 hours ago by 50k • written 1 day ago by • 0
0
votes
1
reply
10
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated just now by 65k • written 1 hour ago by • 0
0
votes
1
reply
72
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 23 hours ago by 50k • written 1 day ago by • 0
14 results • Page 1 of 1
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Replies
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…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
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
stuck on unimplemented type 'list' in 'EncodeElement'
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