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pvalue
•
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0
votes
0
replies
161
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
5 months ago
Tadeoye
• 0
0
votes
1
reply
936
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 22 months ago by
ATpoint
★ 3.4k • written 22 months ago by
Johan Largo
• 0
1
vote
2
replies
729
views
How to understand the P-value generated by DEseq2
pValue
updated 2.4 years ago by
Michael Love
40k • written 2.4 years ago by
Kai_Qi
▴ 20
0
votes
6
replies
1.2k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
4.4 years ago
fiona.dick91
▴ 60
0
votes
6
replies
1.2k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 4.5 years ago by
Michael Love
40k • written 4.5 years ago by
peibo_xu
• 0
1
vote
5
replies
1.8k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 4.6 years ago by
Gordon Smyth
48k • written 4.6 years ago by
xingxd16
▴ 20
0
votes
8
replies
9.6k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
updated 4.6 years ago by
Michael Love
40k • written 4.6 years ago by
ricardo3889
• 0
4
votes
7
replies
1.9k
views
edgeR DEG glmQLFTest
glmQLFTest
pvalue
updated 4.7 years ago by
Gordon Smyth
48k • written 4.7 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
707
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 4.9 years ago by
Michael Love
40k • written 4.9 years ago by
oscarf
• 0
9
votes
5
replies
3.6k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 4.9 years ago by
Steve Lianoglou
13k • written 4.9 years ago by
Harrisonesmith
• 0
4
votes
4
replies
1.5k
views
What doest this p.value distribution mean?
deseq2
pvalue
updated 5.3 years ago by
Michael Love
40k • written 5.3 years ago by
chipolino
• 0
1
vote
1
reply
1.0k
views
fdrtool corrected p-value histograms look weird
pvalue
adjusted pvalue
fdrtool
updated 5.6 years ago by
Michael Love
40k • written 5.6 years ago by
hele7
▴ 20
2
votes
2
replies
1.8k
views
How to control p-value inflation with limma
limma
pvalue
inflation
bacon
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
stephane.cauchi
▴ 10
1
vote
1
reply
2.4k
views
Q value obtained from QValue package is lower than P value?
qvalue
pvalue
r
multiple comparisons
updated 6.7 years ago by
Storey, John D.
▴ 90 • written 6.7 years ago by
tombernardryan
▴ 50
0
votes
1
reply
1.1k
views
meta analysis of clc output(differential expression data )
rnaseq
metaseq
clc output
pvalue
meta analysis
updated 6.7 years ago by
Koki
▴ 10 • written 6.7 years ago by
hassangiahi
• 0
2
votes
10
replies
8.0k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 7.0 years ago by
Michael Love
40k • written 7.0 years ago by
fromhj304
▴ 10
2
votes
4
replies
1.1k
views
ResrtingTools include pvalue NA
reportingtools
deseq2
NA
pvalue
updated 7.3 years ago by
Michael Love
40k • written 7.3 years ago by
NMostajo
▴ 10
0
votes
8
replies
1.5k
views
ReportingTools include pvalue NA and comparissons
R
reportingtools
deseq2
pvalue
coef
updated 7.3 years ago by
Michael Love
40k • written 7.3 years ago by
NMostajo
▴ 10
4
votes
1
reply
1.5k
views
Very low EdgeR Pvalues with very small sample size
edger
pvalue
sample size
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
Venu Pullabhatla
▴ 40
6
votes
8
replies
5.0k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 10 months ago by
James W. MacDonald
63k • written 7.5 years ago by
serpalma.v
▴ 60
7
votes
11
replies
3.2k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 7.6 years ago by
James W. MacDonald
63k • written 7.6 years ago by
enricoferrero
▴ 660
1
vote
2
replies
1.2k
views
Cannot re-create q-values from the p-values in the DiffTable.
cummeRbund
pvalue
adjusted pvalue
qvalue
updated 7.7 years ago by
James W. MacDonald
63k • written 7.7 years ago by
Sameet Mehta
▴ 30
0
votes
0
replies
933
views
pvalRRHO() does not compute the p-value
RRHO
rank
pvalue
8.0 years ago
aurelien
▴ 10
1
vote
3
replies
1.6k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
amoltej
▴ 10
4
votes
5
replies
2.6k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 8.3 years ago by
svlachavas
▴ 810 • written 8.3 years ago by
Agaz Hussain Wani
▴ 260
25 results • Page
1 of 1
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Replies
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Shihui
• 0
It makes sense that DeSeq2 normalized FPMs are more accurate. Thank you for the information!
Answer: DiffBind - how to prep the sample matrix when multiple bam files are used by MAC
by
James W. MacDonald
63k
If you essentially combined multiple BAM files in the MACS call, you could then just combine them using `samtools cat`, in which case you o…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Michael Love
40k
I can rephrase your question as: Why is number of reads not the superior estimate for the scaling factor (the "m" in rpm). There are som…
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
by
Shihui
• 0
Hi Michael, Yes I manually calculated the RPMs by dividing each genes RPM to the library read depth. I didn't do any other normalization …
Comment: shinyMethyl - saving the file
by
dorota.komar
• 0
I tried printing the page as pdf, unfortunately I get the same problem. I guess for now, I will need to save the graphs separately :) Than…
Votes
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Batch correction and Deseq2
A: Read counts between QSEA and MEDIPs
ComBat_seq function in sva package does not return a matrix
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