0
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3
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4.3k
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how to use Normalized gene expression data in Deseq2?
Deseq2
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 10
0
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0
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1.4k
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Error processing Infinium 450K Methylation data using Minfi
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10.0 years ago pm2015 • 0
0
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0
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News: bioconductor.org scheduled downtime, Thursday, December 31st, 12:01PM PST
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10.0 years ago Dan Tenenbaum ★ 8.2k
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1
reply
853
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making a factor numeric
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10.0 years ago Angel ▴ 40
0
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1
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1.5k
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Using dispersion per gene to run Wald test (DESeq2)
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updated 10.0 years ago by 43k • written 10.0 years ago by • 0
2
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2
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1.6k
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Is shellinabox support a feature of all Bioconductor Amazon Machine Images?
ami
updated 10.0 years ago by ★ 8.2k • written 10.0 years ago by • 0
0
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1
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1.5k
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Error with SCAN.UPC UPC_RNASeq method
scan.upc RNA-Seq UPC
10.0 years ago vn • 0
2
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2
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1.7k
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I'm looking for a filtering method that it does't use genewise variances
genefilter liimma microarray
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 20
0
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1
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1.1k
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problem in biophysconnector package
software error
10.0 years ago Angel ▴ 40
0
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1
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1.5k
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Converting Mascot.dat files to csv
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10.0 years ago paul.jenoe • 0
0
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9
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7.4k
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unable to update mgcv package
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updated 10.0 years ago by 25k • written 10.0 years ago by • 0
0
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4
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edgeR Code syntax for without replicate
edger
updated 10.0 years ago by ★ 29k • written 10.0 years ago by • 0
4
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4
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2.8k
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Suggestions for non-specific filtering criteria with limma
limma genefilter
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ▴ 10
3
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3
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2.3k
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Read in specific rows of a BAM file that match a certain RNAME
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updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 50
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2
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1.6k
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Error in heatmap()
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updated 10.0 years ago by 68k • written 10.0 years ago by • 0
3
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7
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3.1k
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Dealing with missing samples in limma and design matrix questions
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10.1 years ago • updated 10.0 years ago clevy ▴ 10
7
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16
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3.3k
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Can "Glue Grant" arrays be processed with pd.hta.2.0?
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updated 10.0 years ago by 68k • written 10.0 years ago by ★ 3.4k
13
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3
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5.0k
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EdgeR cpm: factor of 2 when adjusting library size?
edger cpm
10.0 years ago mikaelhc ▴ 20
0
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1
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3.1k
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AnnotationHub - Problem with SSL CA certificate
annotationhub dependencies
10.0 years ago dalloliogm ▴ 50
0
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1
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876
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Modify column names of big data frame
annotation
updated 10.0 years ago by ▴ 370 • written 10.0 years ago by ▴ 10
6
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5
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2.6k
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Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
10.0 years ago Pierre-François Roux • 0
0
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0
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1.5k
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Question about lumiT warning message
lumi
10.0 years ago clevy ▴ 10
0
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7
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2.1k
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errors for goseq makeOrgPackageFromNCBI in AnnotationForge
go
updated 10.0 years ago by 68k • written 10.1 years ago by • 0
2
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7
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3.4k
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edgeR for with no Replicate
edger without replicate
updated 10.0 years ago by ▴ 900 • written 10.0 years ago by • 0
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0
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ChAMP MDS 1000 most variable positions
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10.0 years ago Eric Smith • 0
0
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5
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5.5k
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how to design a formula in DEseq2 that control for the effect of putative confounders?
Deseq2 dds confounders
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 30
0
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5
replies
5.5k
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Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixe…
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12.5 years ago • updated 4.0 years ago Gordon Smyth 53k
0
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0
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1.4k
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Job: Looking for several bioinformaticians up to the level of Research Assistant Professor
bioinformatician job Job
10.0 years ago Julie Zhu ★ 4.3k
4
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9
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9.7k
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Upper triangular matrix heatmap using pheatmap package
pheatmap
10.0 years ago Deepak Tanwar ▴ 10
0
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8
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1.9k
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Get ID Mapping right
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updated 10.0 years ago by 68k • written 10.0 years ago by • 0
0
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2
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DiffBind: correlation heat map
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updated 10.0 years ago by ★ 5.2k • written 10.0 years ago by • 0
1
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3
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DESeq2: deduce variable for design formula based on sample_info columns (Rscript)
deseq2
updated 10.0 years ago by 43k • written 10.0 years ago by • 0
0
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1
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1.5k
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UPC RNA-Seq individual samples
scan.upc upc rnaseq
updated 10.0 years ago by ▴ 600 • written 10.0 years ago by ▴ 30
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4
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diffbind and macs2 output
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updated 10.0 years ago by ▴ 670 • written 10.0 years ago by ▴ 10
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2
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How do I retrieve consensus peakset?
diffbind peakset
updated 10.0 years ago by ▴ 670 • written 10.0 years ago by • 0
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6
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failed to load 'AnnotationHub' resource
annotationhub annotation error
10.0 years ago elhananby ▴ 10
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Error in MetaQC R package.
r metaqc microarray geneexpression
10.0 years ago Agaz Hussain Wani ▴ 260
0
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1
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2.8k
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Bioconductor installation problem
installation biocLite
updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 10
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RSubread 0% mapping
rsubread mapping featurecounts align
10.0 years ago Jo ▴ 30
5
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3
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BLAST in R
updated 10.0 years ago by ▴ 20 • written 14.6 years ago by ▴ 20
1
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2
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2.2k
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BiocParallel::bplapply() performance issue
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updated 10.0 years ago by 25k • written 10.0 years ago by ▴ 30
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3
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ggbio circular plot
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updated 10.0 years ago by ★ 11k • written 10.0 years ago by • 0
5
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7
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Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 270
2
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6
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Understanding and creating various comparisons with model.matrix in limma regarding microarrays
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10.0 years ago Konstantinos Yeles ▴ 90
1
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1
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1.7k
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embed url in pathview images
pathview r pdf kegg graphviz
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by • 0
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DMRcate error: object 'annotated' not found
dmrcate error
updated 10.0 years ago by ▴ 230 • written 10.0 years ago by • 0
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7
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GO.db installation error
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updated 10.0 years ago by • 0 • written 10.1 years ago by • 0
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CEL to Cibersort mix files, fails find Affymatrix specs
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10.1 years ago • updated 10.0 years ago thrabe • 0
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Saving the CSAW results to file
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updated 10.0 years ago by ★ 29k • written 10.0 years ago by ▴ 30
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2
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Exclude masked rownames in DNAMultipleAlignments
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updated 10.0 years ago by ★ 6.8k • written 10.0 years ago by ▴ 30
46,699 results • Page 420 of 934
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Comment: blockwiseModule crashes in the end and doesn't generate modules by gexose2839 • 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA? by TikTsokaasocissalpc • 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
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Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. The prob…
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
Discover the pinnacle of Brazilian Jiu Jitsu gear at [Dragon][1] GI. [1]: https://dragongi.com/
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
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Answer: Large logFC but somewhat high FDR
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