Showing : process • reset
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Error with getBM: 'The query to the BioMart webservice returned an invalid result.'
process annotationTools AnnotationFilter Annotation biomaRt
2.4 years ago Shane • 0
4
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8
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Designing a model matrix and further process?
limma annotation R process
6.8 years ago Biotechuos4 • 0
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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
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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
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965
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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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840
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Use of the GeneMeta package
process
7.5 years ago m.batzenschlager • 0
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about keeping the processing results in the computer memory
process
7.6 years ago Bogdan ▴ 670
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1.2k
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Help for affy
affy process probe
8.2 years ago weizhong_2007 • 0
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1
reply
1.6k
views
champ package input
process
updated 9.5 years ago by 6.7k • written 9.5 years ago by • 0
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2
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5.8k
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read .mat file in R
process
updated 9.6 years ago by ★ 3.0k • written 9.6 years ago by • 0
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1
reply
1.7k
views
MEDIPS quality control
process medips
updated 9.5 years ago by ▴ 570 • written 9.6 years ago by • 0
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2
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3.8k
views
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
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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
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2.3k
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.7 years ago Bernd Fischer ▴ 550
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4
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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
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2
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1.2k
views
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
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1
reply
2.3k
views
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
reply
2.3k
views
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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6
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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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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
0
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1
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1.3k
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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
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1.2k
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rhdf5 read/write concurrency surprise
GO rhdf5 PROcess GO rhdf5 PROcess
9.8 years ago Brad Friedman ▴ 40
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1
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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
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2
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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
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1
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1.2k
views
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
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0
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1.2k
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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
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0
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1.5k
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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
2
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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
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0
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1.3k
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Rgraphviz compilation error
graph Rgraphviz PROcess graph Rgraphviz PROcess
10.0 years ago Kasper Daniel Hansen ★ 6.5k
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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
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2.1k
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Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
10.0 years ago Elena Serrano ▴ 30
0
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1
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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
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0
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740
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strange spam from biocbuild
PROcess PROcess
10.0 years ago Marc Carlson ★ 7.2k
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1
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1.0k
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help needed with the design matrix
PROcess edgeR PROcess edgeR
updated 10.0 years ago by 65k • written 10.0 years ago by ★ 13k
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5
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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
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1
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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
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0
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1.3k
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Factor-related problem when creating new flowFrame
PROcess PROcess
10.1 years ago Kipper Fletez-Brant ▴ 150
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1.0k
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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
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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
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0
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1.5k
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data process before overlap analysis with the DiffBind
PROcess DiffBind PROcess DiffBind
10.1 years ago Rory Stark ★ 5.2k
0
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1
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1.8k
views
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
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3
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1.2k
views
recommend package for exon array analysis
PROcess PROcess
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ★ 13k
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0
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2.2k
views
GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
GO Organism PROcess goseq GO Organism PROcess goseq
10.1 years ago Dale Richardson ▴ 30
0
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1
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1.3k
views
VSN after xps with RaGene2.0ST chips - is there a way to keep an identifier?
vsn PROcess xps vsn PROcess xps
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 350
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0
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893
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question regarding function IMA.methy450PP in IMA package
PROcess PROcess
10.2 years ago Jack Luo ▴ 440
0
votes
12
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2.9k
views
bumphunter DMRs difficulties
PROcess minfi bumphunter PROcess minfi bumphunter
updated 10.2 years ago by ★ 6.5k • written 10.2 years ago by ▴ 160
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votes
2
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2.3k
views
Limma design : What is the "best" method to infer biological replicates during differentially expression analysis
Microarray limma PROcess Microarray limma PROcess
updated 10.2 years ago by 50k • written 10.2 years ago by ▴ 20
1
vote
3
replies
1.5k
views
RMA on Exon Array NaN values
Normalization PROcess Normalization PROcess
updated 10.2 years ago by ★ 4.3k • written 10.2 years ago by ▴ 40
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votes
2
replies
1.3k
views
Tigre Package question 3
Microarray impute PROcess convert mmgmos puma tigre trigger Microarray impute PROcess
updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 50
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0
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967
views
FW: Tigre Package question 3
impute PROcess mmgmos puma impute PROcess mmgmos puma
10.2 years ago Solanki, Anisha ▴ 60
50 results • Page 1 of 1
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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