Showing : affy • reset
6
votes
8
replies
2.5k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
6.4 years ago Jurat Shahidin ▴ 80
1
vote
2
replies
1.2k
views
"hgu133plus2db" package not working in R
microarray affy annotation
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
2
votes
8
replies
1.9k
views
affycoretools package, HTA 2.0 annotation query
annotation affy
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 10
0
votes
0
replies
872
views
table (pData(eset_NONE)[,"Study"]); table(pData(eset_NONE)[,"Disease"]);
affy insilicomerging
6.6 years ago pratikshasharma47 • 0
0
votes
0
replies
1.0k
views
How to color samples in boxplot based on treatment or control using covdesc file
affy boxplot
6.6 years ago pratikshasharma47 • 0
3
votes
5
replies
1.6k
views
HTA 2.0 Differential expression analysis - design question
limma hta affy annotation
updated 6.6 years ago by 68k • written 6.6 years ago by ▴ 10
0
votes
1
reply
959
views
Differentially expressed genes in rice affymetrix data and annotation
affy microarray differentially expresed genes limma annotation
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
vote
1
reply
935
views
Microaaray data analysis
affy
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
votes
0
replies
843
views
fData slot in gene expression analysis
affy microarray gene expression analysis
6.6 years ago pratikshasharma47 • 0
1
vote
1
reply
1.4k
views
Error in getBM(c("affy_rice", "ensembl_gene_id", "entrezgene", "external_gene_name"), : could not find function "featureNames"
annotation error biomaRT affy ricedataset
updated 6.6 years ago by ★ 6.6k • written 6.6 years ago by • 0
3
votes
2
replies
7.0k
views
run affy package encounts clariomdhumancdf error
affy getCdfInfo(object) CDF environment Clariom_D_Human
updated 6.7 years ago by ★ 4.1k • written 6.7 years ago by • 0
1
vote
6
replies
1.8k
views
Error while running affylmGUI
microarray limma affy affylmGUI
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1
vote
1
reply
810
views
"0" p value from Rosetta resolver?
microarray affy
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
votes
2
replies
1.3k
views
Need expert suggestion about Bioconductor package for microarray data anlaysis
affy limma
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
votes
0
replies
1.4k
views
ath1121501probe_1.0 error (was GCRMA missing value error on ATH1 chip)
probe affy probe affy
updated 6.8 years ago by 0 • written 21.7 years ago by ▴ 940
0
votes
1
reply
2.1k
views
gcrma background correction-saving output
cdf affy gcrma matchprobes affyio cdf affy gcrma matchprobes affyio
updated 6.8 years ago by 0 • written 18.9 years ago by ★ 2.2k
0
votes
3
replies
4.0k
views
Issue with DESeqDataSetFromMatrix
deseq2 deseqdatasetfrommatrix rnaseq affy
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
votes
5
replies
1.6k
views
Error in get(cdfname, object 'mm430mmentrezgcdf' not found
affy cdf rma
updated 6.9 years ago by ★ 4.1k • written 6.9 years ago by • 0
1
vote
2
replies
881
views
Normalize the raw data from multiple studies
normalization affy
7.2 years ago mahm ▴ 20
1
vote
13
replies
4.3k
views
Using Limma to normalize data sets
limma affy
updated 7.2 years ago by ▴ 160 • written 7.2 years ago by ▴ 20
0
votes
1
reply
1.9k
views
Finding/Understanding Affy 6.0 Annotation File
affy affymetrix microarray SNP
7.2 years ago CantExitVIM ▴ 10
0
votes
1
reply
853
views
Why some packages don't work?
software error bioconductor affy
updated 7.3 years ago by ★ 1.1k • written 7.3 years ago by • 0
1
vote
2
replies
1.1k
views
Affe package mas5 error
affy affy mas5
7.4 years ago yuyingxie • 0
2
votes
2
replies
1.4k
views
Affy's exprs not working.. intensity works..
affy exprs intensity
updated 7.4 years ago by 68k • written 7.4 years ago by • 0
0
votes
1
reply
1.5k
views
Error: 'unknown input format' while trying http://bioconductor.org/packages/3.7/bioc
error oligo affy
7.5 years ago kritikamish99 ▴ 10
4
votes
5
replies
1.9k
views
fRMA results different for Windows and Linux
frma expr gene expression data affy
updated 7.5 years ago by 68k • written 7.5 years ago by • 0
1
vote
2
replies
1.4k
views
affymetrix miRNA microarray analysis, (package mirna30cdf)
microarray affy
updated 7.6 years ago by 68k • written 7.6 years ago by ▴ 20
0
votes
2
replies
3.8k
views
Can't Use "getGEO" Command Function in R Program
microarray software error bioconductor affy R
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
0
votes
3
replies
1.5k
views
How to bypass ReadAffy warning
affy
7.6 years ago joseph.a.white1 • 0
0
votes
8
replies
4.9k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.6 years ago by • 0 • written 11.7 years ago by ▴ 300
2
votes
2
replies
3.3k
views
Issue with 'Could not obtain CDF environment' after attempting to extract information out of an AffyBatch object
Affy cdf .cel
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
vote
6
replies
2.9k
views
How to process Affymetrix HT HG-U133+ PM Array Plate
affy affymetrix microarrays preprocessing
updated 7.6 years ago by ★ 4.1k • written 7.6 years ago by ▴ 260
2
votes
3
replies
3.2k
views
hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
readaffy frma affy package installation hgu133a
7.6 years ago Chris Mancuso • 0
0
votes
2
replies
2.1k
views
AffyBatch and ArrayExpress
arrayexpress affy bugs
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 230
0
votes
2
replies
2.6k
views
Affymetrix Mogene 1 0 ST
Annotation Normalization affy Annotation Normalization affy
updated 7.7 years ago by • 0 • written 16.9 years ago by ▴ 30
1
vote
3
replies
2.8k
views
AffyLib query in topGO
topGO affy
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
7
votes
8
replies
2.9k
views
Microarray analysis using RMA method using affy, limma
microarray annotation aureus affy
7.8 years ago • updated 7.7 years ago neranjan007 • 0
0
votes
0
replies
1.6k
views
Interpreting Affymetrix Human Genome U133 Plus 2.0 samples
gene expression gene expression data cel affy affymatrix
7.8 years ago torgeirous • 0
0
votes
1
reply
1.1k
views
Affy ClariomD human transcriptome annotation
affy annotation pd.clariom.d.human
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
0
votes
2
replies
3.2k
views
Processing array with R
cdf software error affy R
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
5
votes
4
replies
4.1k
views
How to use custom cdf "hgu133plus2hsentrezgcdf"?
customcdf affymetrix microarrays hgu133plus2 affy
7.8 years ago rahil ▴ 30
0
votes
1
reply
1.0k
views
R version and packages problems
affy bioconductor microarray
7.9 years ago amaalkalds • 0
0
votes
2
replies
1.3k
views
Some questions about chip quality control
affy
updated 8.2 years ago by ★ 4.1k • written 8.2 years ago by ▴ 10
3
votes
5
replies
1.8k
views
Some doubts about the limma package
limma affy
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
1
vote
6
replies
1.7k
views
Why can't I use the same R package to get the same conclusions as the author?
limma affy
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 10
7
votes
7
replies
2.5k
views
Identify up and down regulated genes in affymetrix data
limma microarray affy
updated 8.3 years ago by ▴ 40 • written 8.3 years ago by • 0
0
votes
7
replies
2.3k
views
oligo and GenericPDInfo
affy oligoclasses oligo package pdinfobuilder annotationdbi
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 510
6
votes
8
replies
3.0k
views
Gene level analysis of Affymetrix GeneChip Mouse Exon Arrays
affy aroma.affymetrix exon array xps oligo
8.3 years ago Gordon Smyth 53k
3
votes
2
replies
1.5k
views
RankProd throws "is.infinite(data)" error for type "S4" for differential expression analysis
rankprod limma affy bioconductor microarray
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 20
0
votes
4
replies
2.0k
views
how to normalize mogene 2.1 st array?
affy
10.9 years ago • updated 8.4 years ago aritra • 0
1,805 results • Page 2 of 37
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Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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