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DeSeq2
•
reset
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
2
votes
9
replies
337
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
Alexandre
• 0
1
vote
4
replies
294
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
7 days ago • updated 6 days ago
winwater0928
• 0
1
vote
4
replies
438
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 12 hours ago
JKim
• 0
0
votes
3
replies
172
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 9 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
3
votes
3
replies
189
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
1
vote
3
replies
183
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 5 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
2
replies
178
views
PCA plot suggestions
DESeq2
PCAtools
updated 5 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
2
replies
689
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
14 days ago • updated 5 days ago
ussarizona
▴ 10
0
votes
1
reply
65
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Aurora
• 0
0
votes
1
reply
72
views
putting my own expression data in deseq2
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 1 day ago by
Dev
• 0
0
votes
1
reply
78
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
1
vote
1
reply
73
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
marcusn
• 0
0
votes
1
reply
82
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 10 hours ago by
ATpoint
★ 4.1k • written 10 hours ago by
angelathuynh5
• 0
0
votes
0
replies
16
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
8 hours ago
kcarey
• 0
0
votes
0
replies
19
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
8 hours ago • updated 7 hours ago
james.zhang20
• 0
16 results • Page
1 of 1
Recent ...
Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
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…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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