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dese
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4
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4
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1.1k
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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 12 months ago by
Bernardo
▴ 10
3
votes
3
replies
924
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
977
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
799
views
DESeq2 analysis
DESe
DESeq2
9 months ago • updated 8 months ago
Adèle
• 0
0
votes
2
replies
845
views
DESeq2 ratio of ratios and p-value
DESeq2
dese
2.5 years ago
wilfried.guiblet
• 0
0
votes
2
replies
246
views
Cross-species analysis using DESeq2 - size factor computation
dese
DESeq2
3 months ago • updated 12 weeks ago
pl23
• 0
0
votes
2
replies
393
views
Linear Model Fitting and Colinearity
dese
DESeq2
4 months ago
Hugo
• 0
0
votes
2
replies
757
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
243
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
618
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
161
views
collapseReplicates dimension error
DESeq2
Dese
updated 4 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 23 months ago by
Maryam.sed1400
• 0
0
votes
2
replies
945
views
Handling NA's in Deseq2
Dese
DESeq2
10 months ago
Asger Mølgaard
• 0
15 results • Page
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Replies
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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