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CRISPRseek: searchHits() optimization
Preprocessing BSgenome safe BSgenome CRISPRseek Preprocessing BSgenome safe BSgenome
9.7 years ago Julie Zhu ★ 4.3k
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Aha: different error may be a clue: RE: separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
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separate MEDIPS.createSet required for each replicate? RE: using custom BSgenome with MEDIPS
Alignment BSgenome safe BSgenome MEDIPS Alignment BSgenome safe BSgenome MEDIPS
updated 10.4 years ago by ▴ 570 • written 10.4 years ago by ▴ 220
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GWASTools suggestions: explicit interface for GenotypeReaders,
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updated 10.4 years ago by ▴ 870 • written 10.4 years ago by ▴ 70
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SAM for protemics - low q values
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10.6 years ago Hendrik Nolte ▴ 10
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DEXSeq on two-exon genes: how to specify a formula without redundant terms
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10.9 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
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BitSeq: Required input for 3' bias correction on transcripts.
Transcription RNASeq safe BitSeq Transcription RNASeq safe BitSeq
11.2 years ago Peter Glaus ▴ 70
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Log transformation and left censoring
limma safe edgeR limma safe edgeR
11.2 years ago Paul Harrison ▴ 100
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BitSeq: Required input for 3' bias correction on transcripts.
RNASeq safe BitSeq RNASeq safe BitSeq
11.2 years ago Dave Gerrard ▴ 40
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frma for Nimblegen arrays?
Microarray Annotation Normalization affy PROcess safe frma frmaTools Microarray affy
updated 11.5 years ago by ★ 4.3k • written 11.5 years ago by ▴ 260
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SCAN UPC probability - validation of gene expression results using UPC
hgu133a2 safe SCAN.UPC hgu133a2 safe SCAN.UPC
updated 11.5 years ago by ▴ 590 • written 11.5 years ago by ▴ 850
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SCAN UPC probability - validation of gene expression results using UPC
hgu133a2 safe hgu133a2 safe
11.5 years ago Guest User ★ 13k
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5
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1.4k
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frma for Nimblegen arrays?
Microarray Normalization affy PROcess safe frma Microarray Normalization affy PROcess
updated 11.5 years ago by ▴ 830 • written 11.5 years ago by ▴ 260
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flowCore 1.22.0 broken for some FCS files
Cancer safe flowCore Cancer safe flowCore
11.9 years ago Josef Spidlen ▴ 140
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1.2k
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dbSNP strand information
SNPlocs safe SNPlocs safe
12.2 years ago Alex Gutteridge ▴ 650
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3
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1.5k
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Strand information for dbSNP packages
SNPlocs safe SNPlocs safe
updated 12.2 years ago by ★ 6.8k • written 12.2 years ago by ▴ 650
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Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
safe BiocInstaller safe BiocInstaller
12.4 years ago Firas Swidan ▴ 50
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Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
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12.4 years ago Andrea Grilli ▴ 240
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Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script
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updated 12.4 years ago by ★ 8.2k • written 12.4 years ago by ▴ 50
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1
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Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
updated 12.8 years ago by ▴ 590 • written 12.8 years ago by ★ 2.3k
0
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5
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1.5k
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Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe limma safe ArrayExpress Normalization probe limma safe ArrayExpress
updated 13.0 years ago by ★ 3.6k • written 13.0 years ago by ▴ 220
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0
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1.0k
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Can't reproduce assessment data included in affycomp package
Cancer affy affycomp PROcess safe Cancer affy affycomp PROcess safe
13.0 years ago Harris A. Jaffee ▴ 590
0
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0
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877
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Can't reproduce assessment data included in affycomp package
Cancer affycomp PROcess safe Cancer affycomp PROcess safe
13.0 years ago Philippe Serhal ▴ 10
0
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1
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1.5k
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Combining data from different versions of Illumina HumanHT-12 v3
Normalization probe safe ArrayExpress Normalization probe safe ArrayExpress
updated 13.0 years ago by ★ 3.6k • written 13.0 years ago by ▴ 220
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4
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4.4k
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Bioconductor with Affymetrix Mouse Gene 1.0 ST
Annotation cdf PROcess safe Annotation cdf PROcess safe
13.1 years ago M. Emily Merrill ▴ 20
0
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3
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1.1k
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Package xps - Problem accessing README file
safe xps safe xps
updated 13.4 years ago by ★ 3.9k • written 13.4 years ago by ★ 8.2k
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0
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665
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Now you can smoke anywhere you want!
Cancer safe Cancer safe
14.6 years ago inLife E-Cigarettes ▴ 10
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651
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You Don't Have to Quit Smoking. New Technology!
Cancer safe Cancer safe
14.6 years ago inLife E-Cigarettes ▴ 10
0
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0
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772
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biomaRt - current devel version of biomaRt+RCurl don't work
biomaRt safe biomaRt safe
14.9 years ago Patrick Aboyoun ★ 1.6k
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RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'
Cancer RdbiPgSQL safe Cancer RdbiPgSQL safe
15.0 years ago Ben Madin ▴ 20
0
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2
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899
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RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character'
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updated 15.0 years ago by 16k • written 15.0 years ago by ▴ 20
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646
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!SPAM: Sale Offer:- ViagraCializ Pills at LowestPrices on net! $1.31/tab, find out more ewlelk 6qu
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15.4 years ago Anisa Gracie ▴ 10
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1
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2.0k
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Important information (Discover The Ways That We Protect Your Online Access)
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15.9 years ago �2008 HALIFAX SECURITY ▴ 20
0
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4
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1.5k
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About beadarray normaliseIllumina() warning messages
Normalization GO safe beadarray lumi Normalization GO safe beadarray lumi
updated 16.3 years ago by ▴ 410 • written 16.3 years ago by ▴ 150
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1
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1.3k
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[R] Why SAM has totally diffent results in R2.1.1 and R2.4.0
Microarray Genetics Survival multtest siggenes safe Microarray Genetics Survival multtest
updated 17.4 years ago by ▴ 900 • written 17.4 years ago by 25k
0
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2
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1.6k
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BH vs BY in p.adjust
Coverage limma safe Coverage limma safe
updated 17.8 years ago by ★ 13k • written 17.8 years ago by ▴ 50
0
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5
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1.3k
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Missing chromosomal locations in hgu133a package
hgu133a AnnBuilder safe hgu133a AnnBuilder safe
updated 17.8 years ago by ▴ 870 • written 17.8 years ago by ▴ 60
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1
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1.0k
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limma 3-way interaction
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17.9 years ago Jacob Michaelson ▴ 320
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6
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1.1k
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Limma: background correction. Use or ignore?
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updated 18.1 years ago by ★ 2.4k • written 18.1 years ago by ★ 1.9k
0
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2
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1.2k
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GeneSpring can call R functions?
GO GeneSpring safe GO GeneSpring safe
updated 18.9 years ago by ★ 1.1k • written 18.9 years ago by ▴ 250
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2
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1.1k
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trouble with yeastann function in AnnBuilder
Annotation Yeast probe AnnBuilder safe Annotation Yeast probe AnnBuilder safe
updated 19.2 years ago by ▴ 10 • written 19.2 years ago by ▴ 320
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2
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1.3k
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Bioconductor data sets - Unigene IDs
probe safe probe safe
updated 21.6 years ago by ★ 2.3k • written 21.6 years ago by ★ 13k
42 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
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Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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