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rnaseq_analysis
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limma - Multi-level Experiments - time course data
limma
limma voom
rnaseq_analysis
DEG
6.1 years ago • updated 5.1 years ago
SPbeginner
• 0
1
vote
3
replies
1.3k
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Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis
KEGG
nonmodel species
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
laural710
• 0
0
votes
0
replies
912
views
Sequence composition effect
sequencing
rnaseq_analysis
6.3 years ago
alemutak
• 0
1
vote
3
replies
1.4k
views
RNASeq data analysis with bio replicates
rnaseq_analysis
6.9 years ago
fakhter1
• 0
1
vote
1
reply
1.0k
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How to simulate count data to test rnaseq analysis code?
rnaseq_analysis
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
kjo
▴ 70
3
votes
3
replies
4.3k
views
How to do a confounding variable adjustment without using the treatment information?
deseq2
rnaseq_analysis
variancestabilizingtransformation
confounders
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
ompandey
▴ 10
1
vote
2
replies
1.7k
views
Limma model fitting: including and excluding replicates in the model gives different results in RNAseq Analysis
limma
RNAseq_Analysis
model.matrix
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
anver
• 0
7 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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?
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