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DESE
•
reset
4
votes
4
replies
1.1k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 5 weeks ago by
feather-W
• 0 • written 12 months ago by
Bernardo
▴ 10
3
votes
3
replies
922
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
975
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
2.2 years ago
aedavids
▴ 20
0
votes
5
replies
798
views
DESeq2 analysis
DESe
DESeq2
9 months ago • updated 8 months ago
Adèle
• 0
0
votes
2
replies
841
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
2.5 years ago
wilfried.guiblet
• 0
0
votes
2
replies
240
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
12 weeks ago • updated 11 weeks ago
pl23
• 0
0
votes
2
replies
391
views
Linear Model Fitting and Colinearity
dese
DESeq2
4 months ago
Hugo
• 0
0
votes
2
replies
754
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
239
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2
dese
updated 10 weeks ago by
ATpoint
★ 4.0k • written 10 weeks ago by
Xu
• 0
0
votes
2
replies
616
views
where the gene is overexpressed and down regulated while doing DESeq2 analysis
DESe
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
Dinesh
• 0
0
votes
1
reply
157
views
collapseReplicates dimension error
DESeq2
Dese
updated 29 days ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
0
votes
5
replies
3.3k
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 23 months ago by
Maryam.sed1400
• 0
0
votes
2
replies
938
views
Handling NA's in Deseq2
Dese
DESeq2
10 months ago
Asger Mølgaard
• 0
15 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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