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DESe
•
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4
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4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 6 weeks ago by
feather-W
• 0 • written 13 months ago by
Bernardo
▴ 10
3
votes
3
replies
928
views
Merging two plated in R
dese
DESeq2
updated 23 months ago by
James W. MacDonald
65k • written 23 months ago by
lmrogers34
▴ 10
2
votes
17
replies
1.7k
views
lfcshrink error DESeq2
DESeq2
lfcshrink
DESe
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Alina
• 0
2
votes
3
replies
987
views
Single sided P-value for DESeq2 Likelihood Ratio Test
DESeq2
DESe
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
glennli
• 0
1
vote
3
replies
1.4k
views
ERROR: unable to find an inherited method for function ‘dispersions<-’ for signature ‘"DESeqDataSet",
DESeq2
dese
2.3 years ago
aedavids
▴ 20
0
votes
5
replies
806
views
DESeq2 analysis
DESe
DESeq2
9 months ago
Adèle
• 0
0
votes
2
replies
853
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
2.5 years ago
wilfried.guiblet
• 0
0
votes
2
replies
257
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
3 months ago
pl23
• 0
0
votes
2
replies
399
views
Linear Model Fitting and Colinearity
dese
DESeq2
4 months ago
Hugo
• 0
0
votes
2
replies
765
views
Effect of within-group variation on gene expression analysis
DESeq2
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
hpapoli
• 0
0
votes
2
replies
250
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
updated 11 weeks ago by
ATpoint
★ 4.1k • written 11 weeks ago by
Xu
• 0
0
votes
2
replies
625
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
Dinesh
• 0
0
votes
1
reply
166
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Léa
• 0
0
votes
5
replies
3.4k
views
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
DESE
DESeq2
updated 23 months ago by
Basti
▴ 780 • written 24 months ago by
Maryam.sed1400
• 0
0
votes
2
replies
954
views
Handling NA's in Deseq2
Dese
DESeq2
11 months ago
Asger Mølgaard
• 0
15 results • Page
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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…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
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
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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