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EdgeR: setting reference condition and design matrix headers
edgeR
reference
design matrix
multiple factor design
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Ekarl2
▴ 80
3
votes
3
replies
1.8k
views
EnsDb.Rnorvegicus for Rnor6
annotation
db
reference
rnor6
updated 3.8 years ago by
Guido Hooiveld
★ 3.9k • written 3.8 years ago by
keremwai
• 0
0
votes
2
replies
1.1k
views
sigh of log2FC values in DESeq2
sign
FoldChange
DESeq2
reference
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
yampolsk
• 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
3.8 years ago
keremwai
• 0
0
votes
2
replies
1.0k
views
Reference manual for rmr2 package
reference
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Agaz Hussain Wani
▴ 260
0
votes
0
replies
820
views
Setting relevel with the JunctionSeq package
junctionseq
relevel
reference
7.2 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
808
views
Reference for minimum number of probes commonly used for segmentation of microarray data
segmentation
reference
CNA
TCGA
5.2 years ago
jlarsen728
• 0
7 results • Page
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Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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