0
votes
1
reply
18
views
abs() error in rstudio
DESeq2 BiocManager Bioconductor abs() Bioinformatics
updated 6 hours ago by 6.6k • written 7 hours ago by • 0
0
votes
2
replies
43
views
Error when Installing BioConductor Package ('affy')
Bioconductor Install affy
updated 6 hours ago by 6.6k • written 14 hours ago by • 0
0
votes
1
reply
28
views
CAGEr bug report: wrong consensus cluster results
CAGEr
21 hours ago • updated 14 hours ago Meng • 0
0
votes
0
replies
13
views
question about removing both known and unknown confounders
DESeq2 RUVSeq
16 hours ago Lisa • 0
4
votes
7
replies
100
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
16 hours ago • updated 44 minutes ago Sabiha ▴ 10
1
vote
2
replies
36
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
20 hours ago • updated 17 hours ago mohammedtoufiq91 ▴ 10
0
votes
6
replies
111
views
countToFPKM and featureLength
countToFPKM
1 day ago • updated 10 hours ago Morris • 0
0
votes
0
replies
23
views
RNA seq analysis
RNASeq
22 hours ago lesseyl • 0
5
votes
13
replies
172
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors DataFrame haven_labelled haven
updated 13 minutes ago by 16k • written 1 day ago by • 0
0
votes
2
replies
35
views
DESeq2 on multiple sample groups
DESeq2
1 day ago • updated 20 hours ago grsyhhsb • 0
0
votes
1
reply
23
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio isoform
updated 22 hours ago by ★ 1.9k • written 23 hours ago by • 0
0
votes
0
replies
12
views
HMP1-II Metagenomic Data
MicrobiomeData curatedMetagenomicData
1 day ago Pauline • 0
3
votes
7
replies
168
views
Is it possible to convert "DESeq2's normalized counts" to "DEGs"?
DESeq2 raw
updated 1 day ago by ★ 1.2k • written 7 days ago by • 0
0
votes
2
replies
36
views
Differentially expression analysis of orthologous genes between two species
DESeq2 tximport
1 day ago Konstantinos • 0
0
votes
1
reply
74
views
Setting up contrasts within a dataset within conditions (across different genotype) and across conditions (for the same genotype)
DESeq2
updated 1 day ago by 38k • written 2 days ago by • 0
0
votes
0
replies
33
views
EdgeR without replication
Transcriptomics
1 day ago kuttibiotech2009 • 0
0
votes
0
replies
20
views
Reducing dataset size to improve run time for fitGAM in tradeSeq
tradeSeq pseudotime
1 day ago fluentin44 • 0
0
votes
0
replies
16
views
HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 annotation
HiC-DC+ HiCDCPlus
1 day ago Yue • 0
0
votes
3
replies
60
views
Cannot download flowUtils package from Bioconductor 3.16
Bioconductor flowUtils
updated 1 day ago by ★ 5.8k • written 1 day ago by • 0
1
vote
2
replies
658
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ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 1 day ago by ▴ 40 • written 2.6 years ago by ▴ 10
1
vote
2
replies
57
views
Limma-voom - Timepoint by timepoint comparison in timecourse experiment
limma
2 days ago • updated 1 day ago rina ▴ 20
1
vote
1
reply
31
views
Problems installing methylumi package
methylumi
updated 1 day ago by ★ 5.8k • written 1 day ago by • 0
2
votes
3
replies
111
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
2 days ago • updated 1 day ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
34
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 2 days ago by ★ 1.9k • written 2 days ago by • 0
0
votes
1
reply
28
views
ape::dnds produces nan value
R ape dnds nan nanotubes
updated 5 hours ago by 6.6k • written 2 days ago by • 0
0
votes
2
replies
50
views
Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR edge
updated 2 days ago by 46k • written 2 days ago by • 0
0
votes
0
replies
39
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
2 days ago Konstantin • 0
0
votes
1
reply
76
views
How to interpret DESeq2's padj after setting lfcThreshold and the log2FC is greater than lfcThreshold?
DESeq2
updated 3 days ago by 38k • written 4 days ago by ▴ 10
0
votes
2
replies
77
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 2 days ago by ★ 1.9k • written 7 days ago by • 0
0
votes
1
reply
103
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3 days ago by 38k • written 9 days ago by ▴ 70
0
votes
1
reply
75
views
DESeq2, normalization for within-sample comparison, and 3'-end RNAseq data
DESeq2
updated 3 days ago by 38k • written 12 days ago by • 0
0
votes
1
reply
58
views
unable to load edgeR after installing it
edgeR
updated 2 days ago by ★ 1.9k • written 3 days ago by • 0
0
votes
1
reply
71
views
GDCprepare : Error: BiocParallel errors/Error in stopAndCache(title):
BiocParallelerrors
updated 3 days ago by • 0 • written 29 days ago by • 0
4
votes
2
replies
578
views
DESeq2 false positive result?
DESeq2
updated 1 day ago by ★ 1.2k • written 3 days ago by ▴ 10
1
vote
2
replies
82
views
Changing the sample order in the PCA plot
DESeq2
3 days ago • updated 2 days ago turtle888 • 0
0
votes
2
replies
100
views
Remove low-expressed genes in DESeq2?
DESeq2 lowcountgenes deseq2 independent
updated 3 days ago by • 0 • written 5 days ago by • 0
0
votes
0
replies
29
views
Recount3 error with default "recount3_url" option
recount3
3 days ago Cornwell, Adam ▴ 110
2
votes
4
replies
95
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3 days ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
29
views
coexpression networks
WGCNA igraph
3 days ago María José • 0
0
votes
0
replies
30
views
DiffBind: Error in pv$called[, mask] : subscript out of bounds
DiffBind
4 days ago Pablo • 0
0
votes
0
replies
33
views
A question about GWENA R/Bioconductor package
proteomics GWENA Proteomics WGCNA
4 days ago Abdullah • 0
1
vote
7
replies
153
views
query regarding error in installation of "goseq" R bioconductor package
R Bioconductor Install
updated 4 days ago by 3.4k • written 4 days ago by • 0
0
votes
1
reply
69
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 5 days ago by 61k • written 6 days ago by • 0
0
votes
0
replies
37
views
IHW for multiple regression
IHW
5 days ago Tyson • 0
3
votes
3
replies
99
views
question regarding installation of "enrichplot" with BiocManager
R BiocManager install clusterProfiler GO
updated 3 days ago by ▴ 10 • written 5 days ago by • 0
0
votes
1
reply
109
views
NA value in padj but only for certain contrasts
DESeq2
updated 5 days ago by 38k • written 16 days ago by ▴ 10
1
vote
12
replies
354
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 2 days ago by 38k • written 21 days ago by ▴ 660
0
votes
1
reply
106
views
DESeq2 : Using contrast in results vs performing complete independent analysis
DESeq2
updated 5 days ago by 38k • written 21 days ago by • 0
0
votes
2
replies
117
views
Is it correct to plot Log2FC vs adj p-value from Likelihood ratio test?
DESeq2 adjp Volcano LRT
updated 3 days ago by ▴ 10 • written 22 days ago by ▴ 10
0
votes
1
reply
103
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 5 days ago by 38k • written 23 days ago by ▴ 10
43,476 results • Page 1 of 870
Recent ...
Replies
Comment: SV4Vectors DataFrame bug with haven_labelled data by Hervé Pagès 16k
As I said, the right thing to do is to fix `[ `on `haven_labelled` objects in the **haven** package itself. Any attempt to fix this elsewhe…
Comment: SV4Vectors DataFrame bug with haven_labelled data by Hervé Pagès 16k
There seems to be some confusion. It's not about using `drop=TRUE`or `drop=FALSE` on the data.frame or DataFrame that contains `haven_label…
Comment: Can we use rlog or vst data values in limma for differential expression analysis by Sabiha ▴ 10
@gordonsmyth Perhaps shall I need to create a new post for this question?
Comment: SV4Vectors DataFrame bug with haven_labelled data by Daniel E. Weeks • 0
To attempt to fix this, I forked the `S4Vectors` library from BioConductor from here: https://github.com/Bioconductor/S4Vectors Then, in …
Comment: ape::dnds produces nan value by Vincent J. Carey, Jr. 6.6k
You are seeing warnings. `example(dnds)` also produces NaNs. Warnings can occur when the input data don't conform to expectations of the …
Votes
Comment: Can we use rlog or vst data values in limma for differential expression analysis
Struggling with use and interpretation of "Group-specific condition effects, individuals nested within groups"
Can we use rlog or vst data values in limma for differential expression analysis?
Comment: Problems installing methylumi package
Not full rank design using Deseq2
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