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without replicate
•
reset
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.5 years ago by
Camila Orellana
▴ 10
0
votes
10
replies
4.6k
views
DESeq2 analysis without Replicate
without Replicate
deseq2
updated 2.8 years ago by
Michael Love
41k • written 8.4 years ago by
Sushant Pawar
• 0
0
votes
1
reply
612
views
BSmooth does give DMRs without no replicate data sets
bsmooth
without replicate
dimension
5.8 years ago
nilaycan
• 0
0
votes
3
replies
1.0k
views
time-series, no replicates, no control groupe
deseq2
time-series
without replicate
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
bahlv
• 0
1
vote
5
replies
3.0k
views
steps to get up and down regulated genes using DESeq2
deseq2
without replicate
no replicates
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
Tony
• 0
3
votes
6
replies
4.4k
views
Analyzing data without replicates using DiffBind
diffbind
bioconductor
differential binding analysis
without replicate
chipseq
6.4 years ago
Hesh
▴ 10
4
votes
5
replies
2.5k
views
edgeR- DE analysis with no replicates
edger
differential gene expression
without replicate
nested design
help
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
knipehf
• 0
3
votes
6
replies
1.2k
views
Question about edgeR usage with one case and multiple controls
edgeR
differential expression
without replicate
7.9 years ago
gavin.oliver
• 0
0
votes
3
replies
1.4k
views
to call differential peaks among 4 peaksets all together using DiffBind
diffbind
without replicate
updated 8.1 years ago by
Gord Brown
▴ 650 • written 8.1 years ago by
yiweihe
• 0
2
votes
7
replies
2.8k
views
edgeR for with no Replicate
edger
without replicate
updated 8.4 years ago by
Yunshun Chen
▴ 840 • written 8.4 years ago by
Sushant Pawar
• 0
1
vote
1
reply
1.5k
views
edgeR for without Replicate
edger
without replicate
updated 8.4 years ago by
Aaron Lun
★ 28k • written 8.4 years ago by
Sushant Pawar
• 0
11 results • Page
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Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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★ 5.2k
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tangming2005
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James W. MacDonald
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