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snp
•
reset
0
votes
10
replies
1.5k
views
Affymetrix 500k SNP chips -- copy number/LOH/deletions
SNP
SNP
17.7 years ago
Stephen Henderson
★ 1.0k
5
votes
9
replies
4.2k
views
Looking for annotation file for Affymetrix SNP 6.0
copynumber
snp
affymetrix
8.4 years ago
KB
▴ 50
0
votes
4
replies
1.1k
views
Communicating gene-probe relationships to sam
SNP
Biobase
siggenes
SNP
Biobase
siggenes
18.0 years ago
Charles Crane
▴ 30
0
votes
6
replies
1.5k
views
need help for the study design of a RNA-Seq project
SNP
Sequencing
SNP
Sequencing
11.0 years ago
shirley zhang
★ 1.0k
0
votes
4
replies
1.2k
views
GCRMA backgrounds?
SNP
affy
gcrma
SNP
affy
gcrma
updated 19.8 years ago by
Matthew Hannah
▴ 940 • written 19.8 years ago by
Andrew Harrison
▴ 60
0
votes
3
replies
1.2k
views
Binary CDF and CEL files
SNP
cdf
SNP
cdf
19.4 years ago
Christopher, Neil NIH/NCI
▴ 70
0
votes
3
replies
1.4k
views
GWATools use in creating ncdf files
SNP
cdf
GWASTools
SNP
cdf
GWASTools
updated 10.9 years ago by
Sam Rose
▴ 60 • written 10.9 years ago by
Stephanie M. Gogarten
▴ 870
0
votes
4
replies
2.5k
views
Copy number analysis
SNP
affy
SNP
affy
updated 12.1 years ago by
Djork Clevert
▴ 210 • written 12.1 years ago by
Guest User
★ 13k
0
votes
3
replies
1.1k
views
makepackage of affy's 100K and 500K SNP chip
SNP
cdf
SNP
cdf
updated 18.5 years ago by
Celine Carret
▴ 220 • written 18.5 years ago by
Zhang, Jacob Zhongfa
▴ 60
0
votes
6
replies
2.2k
views
dbSNP build for R package SNPlocs.Hsapiens.dbSNP.20080617
SNP
Cancer
SNPlocs
SNP
Cancer
SNPlocs
updated 8.8 years ago by
genefan
• 0 • written 14.9 years ago by
Hervé Pagès
16k
1
vote
6
replies
2.3k
views
Good way to get location of in-del SNPs in UCSC coordinates?
snplocs
snp
9.4 years ago
garrisrg
▴ 10
0
votes
8
replies
1.8k
views
mouse SNPs
SNP
Annotation
GO
HapMap
annotate
SNP
Annotation
GO
HapMap
annotate
13.6 years ago
Glazko, Galina
▴ 350
0
votes
4
replies
1.2k
views
About CLAC package
SNP
affy
SNP
affy
16.5 years ago
affy snp
▴ 640
0
votes
3
replies
1.3k
views
Package for doing Copy number analsysi with LOH
SNP
SNP
updated 11.9 years ago by
Henrik Bengtsson
★ 2.4k • written 11.9 years ago by
Rajan Saini
▴ 10
0
votes
4
replies
1.4k
views
Affy SNP array analysis
SNP
Microarray
Cancer
affy
SNP
Microarray
Cancer
affy
updated 20.6 years ago by
Holger Schwender
▴ 900 • written 20.6 years ago by
James W. MacDonald
65k
3
votes
5
replies
1.6k
views
Understanding PureCN and its germline SNPs
PureCN
germline
SNP
updated 5.9 years ago by
kakbrus
• 0 • written 6.1 years ago by
twtoal
▴ 10
0
votes
7
replies
1.8k
views
segmentation for Affy SNP arrays
SNP
CGH
affy
GLAD
snapCGH
SNP
CGH
affy
GLAD
snapCGH
updated 16.6 years ago by
Rob Scharpf
▴ 250 • written 16.6 years ago by
Yu Chuan Tai
▴ 440
0
votes
5
replies
3.5k
views
Fast way to find which gene a snp located.
SNP
GenomicFeatures
SNP
GenomicFeatures
updated 13.0 years ago by
hind
▴ 10 • written 13.0 years ago by
Fabrice Tourre
▴ 970
0
votes
2
replies
1.2k
views
Problems with oligo and pd.genomewidesnp.6
SNP
Annotation
HapMap
SNP
Annotation
HapMap
updated 15.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.9 years ago by
Jeremy Silver
▴ 10
0
votes
3
replies
7.1k
views
Retrieving SNP rs IDs using biomaRt getBM()
SNP
SNP
updated 11.4 years ago by
Hervé Pagès
16k • written 11.4 years ago by
Guest User
★ 13k
0
votes
3
replies
696
views
Hello
SNP
SNP
updated 10.6 years ago by
Martin Morgan
25k • written 10.6 years ago by
jayakumar sivalingam
▴ 20
0
votes
3
replies
1.0k
views
Overlay Gene Expression on SNP (copy number) data
SNP
SNP
updated 12.0 years ago by
Tengfei Yin
▴ 420 • written 12.0 years ago by
Ekta Jain
▴ 370
0
votes
3
replies
916
views
aCGH package - performance Issues
SNP
Cancer
SNP
Cancer
16.0 years ago
Julian Lee
▴ 140
0
votes
3
replies
1.2k
views
Spatial Correction
SNP
Normalization
affy
oligo
SNP
Normalization
affy
oligo
updated 17.5 years ago by
Matthew Lyon
▴ 120 • written 17.5 years ago by
Justin Borevitz
▴ 170
0
votes
4
replies
1.5k
views
snpStats, read.long, alleles in two columns
SNP
Genetics
snpStats
SNP
Genetics
snpStats
updated 12.1 years ago by
David Clayton
▴ 20 • written 12.1 years ago by
Liz Hare
▴ 30
0
votes
2
replies
884
views
cdfenv files ATTN: James McDonald
SNP
cdf
probe
reposTools
affy
SNP
cdf
probe
reposTools
affy
updated 17.6 years ago by
James W. MacDonald
65k • written 17.6 years ago by
Andrew Van Brunt
▴ 20
0
votes
3
replies
1.2k
views
snpMatrix - Creating a 1-column snp.matrix by subsetting a larger snp.matrix
SNP
SNP
15.9 years ago
Richard Pearson
▴ 390
0
votes
6
replies
5.6k
views
Calculate heterozygosity % using SNP genotype data
SNP
snpMatrix
SNP
snpMatrix
updated 11.8 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.8 years ago by
gowtham
▴ 210
0
votes
5
replies
1.3k
views
Finding coding SNPs with predictCoding
SNP
ctc
SNP
ctc
updated 12.2 years ago by
Thomas Girke
★ 1.7k • written 12.2 years ago by
Valerie Obenchain
★ 6.8k
0
votes
2
replies
6.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP
Sequencing
Coverage
Alignment
Cancer
Biostrings
PROcess
IRanges
GenomicRanges
SNP
updated 10.5 years ago by
Michael Lawrence
★ 11k • written 10.5 years ago by
Hervé Pagès
16k
0
votes
4
replies
1.4k
views
gwSnpTests in GGtools
SNP
GO
SNP
GO
updated 12.4 years ago by
Vincent J. Carey, Jr.
6.7k • written 12.4 years ago by
Guest User
★ 13k
0
votes
3
replies
1.9k
views
[Bioc-sig-seq] Bioconductor 2.8 is released
SNP
Sequencing
miRNA
Microarray
Annotation
Normalization
Pathways
Preprocessing
Survival
updated 13.0 years ago by
Ivan Gregoretti
▴ 310 • written 13.0 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
11
replies
3.5k
views
SNP6 data to VCF
SNP
oligo
ASSIGN
SNP
oligo
ASSIGN
updated 5.6 years ago by
giulio.genovese
• 0 • written 12.2 years ago by
Sean Davis
21k
0
votes
4
replies
1.5k
views
faster way to get differential calls from pileup?
SNP
Sequencing
PROcess
SNP
Sequencing
PROcess
updated 13.5 years ago by
Sean Davis
21k • written 13.5 years ago by
wrighth
▴ 260
0
votes
3
replies
1.4k
views
beadarray illumina Human610-Quadv1_B.bpm
SNP
Annotation
illuminaHumanv1
beadarray
SNP
Annotation
illuminaHumanv1
beadarray
updated 14.0 years ago by
Mark Dunning
★ 1.1k • written 14.0 years ago by
Nolwenn Le Meur
▴ 80
0
votes
4
replies
1.5k
views
Bioconductor 2.8 is released
SNP
Sequencing
miRNA
Microarray
Annotation
Normalization
Pathways
Preprocessing
Network
updated 13.0 years ago by
Ivan Gregoretti
▴ 310 • written 13.0 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
4.7k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Polikepahad, Sumanth
▴ 10
0
votes
3
replies
1.7k
views
readChp (affxparser) segfaults
SNP
cdf
affxparser
SNP
cdf
affxparser
updated 15.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 15.0 years ago by
Gábor Csárdi
▴ 60
0
votes
3
replies
1.0k
views
Fwd: pmStrand() in oligo (version...)
SNP
oligo
SNP
oligo
16.9 years ago
Benilton Carvalho
★ 4.3k
0
votes
3
replies
1.1k
views
smlSet
SNP
HapMap
GGtools
SNP
HapMap
GGtools
updated 14.1 years ago by
Vincent J. Carey, Jr.
6.7k • written 14.1 years ago by
claire pujoll
▴ 30
0
votes
3
replies
3.1k
views
meta-analysis with P values
SNP
SNP
updated 13.8 years ago by
Paul Leo
▴ 970 • written 13.8 years ago by
Laura Rodriguez Murillo
▴ 60
0
votes
2
replies
1.1k
views
Question regarding Affy SNP 5.0/BI_SNP arrays
SNP
Annotation
cdf
affy
PROcess
oligo
SNP
Annotation
cdf
affy
PROcess
oligo
updated 15.0 years ago by
Williams, Alan
▴ 40 • written 15.0 years ago by
Mayer, Claus-Dieter
▴ 120
0
votes
12
replies
2.5k
views
SNP Analysis
SNP
SNP
updated 14.5 years ago by
Claus-Jürgen Scholz
▴ 90 • written 14.5 years ago by
Peter Ganske
▴ 50
0
votes
2
replies
3.8k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 8.8 years ago by
marksteve952
• 0 • written 11.1 years ago by
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
1.3k
views
snpMatrix trouble with read.HapMap.data() and ld.snp()
SNP
convert
SNP
convert
updated 12.8 years ago by
David Clayton
▴ 20 • written 12.8 years ago by
rna seq
▴ 90
0
votes
3
replies
2.0k
views
Welcome to the "Bioconductor" mailing list
SNP
biomaRt
SNP
biomaRt
updated 12.5 years ago by
Ramon Diaz-Uriarte
▴ 70 • written 12.5 years ago by
Adriana Munoz
▴ 100
0
votes
2
replies
1.2k
views
biomaRt doesn't load RCurl automatically
SNP
biomaRt
SNP
biomaRt
15.5 years ago
Shi, Tao
▴ 720
0
votes
2
replies
1.3k
views
LOH analysis for illumina data
SNP
Cancer
Prostate
SNP
Cancer
Prostate
15.7 years ago
Yu Chuan Tai
▴ 440
0
votes
7
replies
1.4k
views
how to put together 600 files from the 5.0 Affy SNPchip
SNP
SNPchip
SNP
SNPchip
15.5 years ago
Laura Rodriguez Murillo
▴ 60
0
votes
3
replies
1.3k
views
Problem with justSNPRMA, library "oligo"
SNP
HapMap
SNP
HapMap
15.2 years ago
alessio boattini
▴ 30
50 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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