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Three questions about processing Agilent Arrays
Normalization limma PROcess Normalization limma PROcess
updated 2.1 years ago by 50k • written 15.2 years ago by ▴ 30
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784
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.5 years ago Shane • 0
0
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4
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19k
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XML package cannot be installed
PROcess PROcess
updated 6.1 years ago by • 0 • written 11.8 years ago by ★ 13k
0
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8
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4.0k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 6.1 years ago by • 0 • written 10.2 years ago by ▴ 300
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1.0k
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deleted questions.. as its not very relevant..
process
6.8 years ago • updated 6.7 years ago bioDoctorate • 0
4
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8
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1.8k
views
Designing a model matrix and further process?
limma annotation R process
6.8 years ago Biotechuos4 • 0
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8
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1.9k
views
raw probe set expression data and masking questions
Normalization Cancer probe affy PROcess Normalization Cancer probe affy PROcess
updated 7.1 years ago by ▴ 40 • written 17.7 years ago by ▴ 20
0
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8
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1.8k
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`bplapply` breaks down (BiocParallel_1.6.6, R 3.3.1, openSUSE Leap)
biocparallel bplapply Suse error process
updated 7.4 years ago by • 0 • written 7.4 years ago by • 0
0
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1
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967
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Error in reading file
process
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by • 0
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0
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843
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Use of the GeneMeta package
process
7.6 years ago m.batzenschlager • 0
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0
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1.1k
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about keeping the processing results in the computer memory
process
7.6 years ago Bogdan ▴ 670
0
votes
7
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2.2k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.7 years ago by • 0 • written 14.0 years ago by ★ 1.6k
2
votes
9
replies
3.4k
views
GEOquery error
Annotation PROcess Annotation PROcess
updated 8.1 years ago by 6.7k • written 10.0 years ago by 65k
0
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0
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1.2k
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Help for affy
affy process probe
8.3 years ago weizhong_2007 • 0
0
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1
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1.2k
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Re: Bioconductor Digest, Vol 24, Issue 11
PROcess PROcess
updated 8.6 years ago by • 0 • written 19.2 years ago by ▴ 320
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2
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1.7k
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 8.7 years ago by • 0 • written 10.1 years ago by ★ 13k
0
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6
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1.9k
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is it possible to find sample batch # in CEL files?
PROcess PROcess
updated 9.0 years ago by • 0 • written 11.3 years ago by ▴ 40
0
votes
2
replies
1.6k
views
Affymetrix file with probe set id
probe affy PROcess probe affy PROcess
updated 9.2 years ago by • 0 • written 19.6 years ago by ▴ 600
0
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1
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1.7k
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Adding Phenodata after processing in Lumi
PROcess lumi PROcess lumi
updated 9.2 years ago by • 0 • written 12.8 years ago by ▴ 10
0
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1
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1.7k
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MEDIPS quality control
process medips
updated 9.5 years ago by ▴ 570 • written 9.6 years ago by • 0
0
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1
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1.6k
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champ package input
process
updated 9.6 years ago by 6.7k • written 9.6 years ago by • 0
1
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2
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5.9k
views
read .mat file in R
process
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
0
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1
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1.8k
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Export mzML via mzR or other bioconductor packages
PROcess mzR PROcess mzR
updated 9.6 years ago by 1.6k • written 10.1 years ago by ★ 13k
0
votes
2
replies
3.8k
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getting normalized expression values from GEO GSE files
PROcess GEOquery PROcess GEOquery
updated 9.7 years ago by ▴ 80 • written 9.7 years ago by ▴ 30
0
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1
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1.5k
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Genes2GO and suggestions to make it faster
Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt
updated 9.7 years ago by 21k • written 9.7 years ago by ▴ 20
0
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0
replies
2.3k
views
rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.8 years ago Bernd Fischer ▴ 550
0
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4
replies
2.2k
views
.cel file processing is not working for an old array
cdf PROcess cdf PROcess
updated 9.8 years ago by 65k • written 9.8 years ago by ▴ 30
0
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2
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1.2k
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xps - error in normalize - "Error: Length of non-varying units is zero."
Normalization PROcess xps Normalization PROcess xps
updated 9.8 years ago by ★ 3.9k • written 9.8 years ago by ▴ 350
0
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6
replies
2.9k
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processing Illumina HT12v4.0 expression data from GEO
Normalization affy PROcess GEOquery frma Normalization affy PROcess GEOquery frma
updated 9.8 years ago by 21k • written 9.8 years ago by ▴ 190
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2.3k
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DESeq2 missing columns
PROcess DESeq PROcess DESeq
updated 9.8 years ago by 41k • written 9.8 years ago by ▴ 20
1
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1
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2.3k
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How to hide or suppress note about ward method in clValid package?
Annotation PROcess Annotation PROcess
updated 9.8 years ago by ★ 1.3k • written 9.8 years ago by ★ 13k
0
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0
replies
1.2k
views
R hthgu133afrmavecs_1.1.0 error: row.effects should sum to zero
GO probe PROcess frma GO probe PROcess frma
9.8 years ago Matthew McCall ▴ 830
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1
reply
1.3k
views
Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 90
0
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0
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1.2k
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.9 years ago Brad Friedman ▴ 40
0
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1
reply
1.9k
views
Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 40
0
votes
2
replies
1.8k
views
xy-plot of fcs fails: undefined column selected
PROcess PROcess
updated 9.9 years ago by ▴ 20 • written 9.9 years ago by ★ 13k
0
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1
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1.2k
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Duplicate probe coordinates with pd.hugene.2.1.st and oligo
probe affy PROcess oligo probe affy PROcess oligo
updated 9.9 years ago by 65k • written 9.9 years ago by ▴ 590
0
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0
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1.2k
views
Issues about how to use rma and paCalls to filter probe sets together
probe PROcess oligo probe PROcess oligo
9.9 years ago 张超 ▴ 50
0
votes
0
replies
1.5k
views
minfi release 1.8
SNP Annotation GO probe SNPlocs PROcess minfi bumphunter ChAMP SNP Annotation GO probe
9.9 years ago swarmqq@gmail.com ▴ 10
0
votes
0
replies
1.3k
views
Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.0 years ago Kasper Daniel Hansen ★ 6.5k
0
votes
0
replies
1.5k
views
Job: Bioinformatics Analyst at Johns Hopkins Medical School (Masters or Ph.D.)
Sequencing Epigenetics PROcess Sequencing Epigenetics PROcess
10.0 years ago Brian Herb ▴ 80
0
votes
0
replies
2.1k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
0
votes
1
reply
3.3k
views
logFC and CPM of edgeR
PROcess edgeR PROcess edgeR
updated 10.0 years ago by ★ 13k • written 10.0 years ago by ★ 13k
0
votes
0
replies
740
views
strange spam from biocbuild
PROcess PROcess
10.0 years ago Marc Carlson ★ 7.2k
0
votes
1
reply
1.0k
views
help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.0 years ago by 65k • written 10.0 years ago by ★ 13k
0
votes
5
replies
1.5k
views
affy( ) error with mas5()
SNP affy PROcess SNP affy PROcess
updated 10.1 years ago by 65k • written 10.1 years ago by ▴ 110
0
votes
1
reply
1.9k
views
Duplicate gene names after summarization with RMA (hugene.1.0.st.v1)
Annotation PROcess Annotation PROcess
updated 10.1 years ago by 65k • written 10.1 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Factor-related problem when creating new flowFrame
PROcess PROcess
10.1 years ago Kipper Fletez-Brant ▴ 150
0
votes
0
replies
1.0k
views
rcModelMedianPolish of the package preprocessCore/ imitate median polish of RMA
Normalization GO probe PROcess Normalization GO probe PROcess
10.1 years ago James W. MacDonald 65k
0
votes
0
replies
1.5k
views
data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
10.1 years ago Rory Stark ★ 5.2k
50 results • Page 1 of 1
Recent ...
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Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
Sorry, for questions about statistical analysis plan and interpretation of results, I recommend to work with a local statistician or someon…
Answer: Fold change calculation in Diffbind vs. DESEQ2? by Michael Love 41k
There was a recent DiffBind question on the support site that noticed the same thing, try searching recent DiffBind posts.
Answer: Timecourse RNASeq analysis by Michael Love 41k
There are many choices for time course, and we have an example in our workflow (rnaseqGene). Otherwise, I recommend to consult a local …
Answer: Padj "NA" with thousands of low count although the raw read counts are quite lar by Michael Love 41k
You can either turn off independent filtering in `results` or use `ihw` see the vignette.
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Thanks Gordon for a detail guide! You have a great memory of time. GSVA also do differential express at pathway level (https://bioconductor…
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Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
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Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
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