5
votes
2
replies
1.1k
views
logo issue: not right handed DNA
bioconductor
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 30
3
votes
2
replies
7.0k
views
Remove one sample from DESeq2 subject
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
0
votes
0
replies
1.0k
views
RIPSeeker problem with the ripseek command
ripseeker AgoIP RIPSeek
8.0 years ago ximena.garate • 0
1
vote
3
replies
880
views
Is it reasonable to use rlog difference to reflect differential expression of a gene across samples, and rlog value to reflect the expression level
deseq2 rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
vote
2
replies
2.2k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
3
votes
4
replies
2.4k
views
Use interactions to get the difference in the effect of two treatments
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 70
1
vote
1
reply
1.5k
views
Unknown gene names in pd.clariom.d.human annotation package
microarray pd.clariom.d.human
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 10
0
votes
0
replies
1.6k
views
Help with generating network from gene expression data
gene expression network cytoscape
8.0 years ago torgeirous • 0
0
votes
0
replies
892
views
How to define data directories and syntax before using readMSData in MSnBase
mzR/ msnBase
8.0 years ago malcolmjctaylor • 0
1
vote
3
replies
3.4k
views
Multiple pairwise comparisons in ballgown
ballgown
updated 8.0 years ago by ▴ 210 • written 8.0 years ago by ▴ 10
1
vote
2
replies
2.0k
views
Error in reading ballgown object
R ballgown
updated 8.0 years ago by ▴ 210 • written 8.0 years ago by • 0
0
votes
0
replies
1.5k
views
CAMERA error - isotopeProportionFits
camera metabolomics
8.0 years ago bhgyu ▴ 30
0
votes
1
reply
1.1k
views
non detects R Package- txt file
non detects qPCRset object software error
updated 8.0 years ago by ▴ 10 • written 8.0 years ago by • 0
0
votes
2
replies
2.8k
views
Creating a qPCRset object from a text file
qPCRset object nondetects r package txt
updated 2.2 years ago by • 0 • written 8.0 years ago by • 0
0
votes
1
reply
2.3k
views
Incorporating 'offset' into edgeR pipeline
edgeR EDASeq offset
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 130
1
vote
1
reply
821
views
What do you do with the DESeq2 NA results ?. How do you manage them ?
DESeq2 NA values
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 130
0
votes
2
replies
2.1k
views
Error in useMart while using a dataset in biomaRt
biomaRt bioconductor celegans annotation
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by • 0
0
votes
4
replies
2.7k
views
biomaRt getBM error in scan
biomart
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by • 0
0
votes
3
replies
2.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
8.0 years ago andrew.gehrke • 0
9
votes
1
reply
5.5k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
0
votes
2
replies
1.5k
views
RUVnormalize- How to output a corrected expression matrix without negative values to use for DEG analysis(i.e. limma) ?
RUVnormalize limma corrected expression matrix microarray
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by • 0
0
votes
3
replies
1.4k
views
exomeCopy error with compileCopyCountSegments
exomecopy cnv
8.0 years ago ramakrishnas • 0
0
votes
5
replies
2.1k
views
CRISPRseek offTargetAnalysis errors
CRISPRseek
8.0 years ago joyce • 0
1
vote
3
replies
1.8k
views
Different microarrays annotations provided by toTable and annotateEset functions
microarray annotation annotationdbi affycoretools annotationtools
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 70
0
votes
1
reply
1.6k
views
Error in export ifelse from IRanges
iranges ifelse package namespace export
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
3
votes
5
replies
1.8k
views
edgeR trended or tagwise
edger glmqlftest()
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 60
0
votes
1
reply
3.5k
views
seqlevels(param) not in BAM header
jmosaics
8.0 years ago james.dalgleish ▴ 30
0
votes
0
replies
834
views
CAMERA fold changes per gene set?
limma
8.0 years ago chris86 ▴ 420
2
votes
5
replies
4.6k
views
Analyse only protein_coding genes
bioconductor edger rna-seq
8.0 years ago martin.weihrauch ▴ 20
0
votes
0
replies
981
views
plotGenes command Sushi
sushi plotGenes
8.0 years ago portia.mcghan • 0
2
votes
3
replies
1.7k
views
voom command broken in limma_3.34.5?
limma voom
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
9
votes
8
replies
7.2k
views
Limma Voom produces many identical adjusted p-values
limma voom adjusted pvalue
updated 8.0 years ago by 53k • written 8.0 years ago by ▴ 370
3
votes
2
replies
1.5k
views
DESeq2 1.16.1 : Zero count values re-occurrence of issue 56191?
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
vote
12
replies
4.9k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2 lfcshrink
8.0 years ago yk.gatc • 0
2
votes
7
replies
2.0k
views
modifying compound datasets
R
8.0 years ago harbydonald • 0
2
votes
4
replies
2.1k
views
Make window around TSS and get values from another data.frame for bins of the specified window
R granges genomicranges chipseq
updated 8.0 years ago by ★ 11k • written 8.0 years ago by ▴ 20
1
vote
1
reply
1.5k
views
seqnames versus chrom
BiocGen rtracklayer genomeinfodb
updated 8.0 years ago by ★ 11k • written 8.0 years ago by • 0
0
votes
0
replies
1.6k
views
Two questions about pathifier package
pathways statistics microarray
8.0 years ago arronar • 0
1
vote
0
replies
2.1k
views
Job: Bioinformatician/Biostatistician - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
rnaseq biostatistics bioinformatician next-generation sequencing Job
8.0 years ago Federico Marini ▴ 180
0
votes
2
replies
1.7k
views
error message from oligo package
oligo
updated 4.4 years ago by • 0 • written 8.0 years ago by • 0
0
votes
1
reply
1.5k
views
ChIPQC Error: subscript contains out-of-bounds ranges
R
updated 3.7 years ago by • 0 • written 8.0 years ago by • 0
1
vote
1
reply
2.6k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
8.0 years ago Stane ▴ 40
2
votes
2
replies
1.2k
views
motifStack: how to make the start of motif logos have the same distance to the center
motifStack
updated 8.0 years ago by ★ 1.3k • written 8.0 years ago by • 0
2
votes
2
replies
2.6k
views
RUVg with differential transcript expression?
ruvseq sleuth
updated 8.0 years ago by ▴ 980 • written 8.0 years ago by • 0
0
votes
2
replies
3.3k
views
Processing array with R
cdf software error affy R
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
0
votes
5
replies
1.2k
views
results function of DESeq2 devel fails
deseq2
8.0 years ago unamourdeswann ▴ 10
0
votes
4
replies
2.2k
views
how to reformat complex list object (derived with TCGAbiolinks)?
TCGA tcgabiolinks list reformat
8.0 years ago Guido Hooiveld ★ 4.1k
2
votes
1
reply
1.7k
views
Build error: could not find function "bplapply"
biocparallel build report
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 180
0
votes
1
reply
1.7k
views
SC3 Package: marker genes and normal genes obtained from featureData
SC3
updated 8.0 years ago by ▴ 150 • written 8.1 years ago by • 0
1
vote
1
reply
1.4k
views
soggi average plot
soggi multiple bam cancer
updated 8.0 years ago by ▴ 10 • written 8.0 years ago by • 0
46,710 results • Page 288 of 935
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
Comment: Guitar R package requires update due to dependency GenomicFeatures by ferran.llobet.cabau ▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub? by Guido Hooiveld ★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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limma moderated t-statistics and B-statistics
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