Showing : gcrma • reset
2
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3
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865
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 12 months ago by 65k • written 12 months ago by ▴ 10
3
votes
4
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1.0k
views
gcrma problem with make.cdf.package
gcrma make.cdf.package affy
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 40
0
votes
1
reply
1.3k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 4.4 years ago by • 0 • written 5.3 years ago by ★ 3.9k
0
votes
2
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851
views
u133aaofav2 platform gcrma Normalization
u133aaofav2 annotation gcrma
4.8 years ago samane.khoshbakht • 0
0
votes
1
reply
607
views
Normalization large data set
normalization gcRMA
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
0
votes
1
reply
1.7k
views
gcrma background correction-saving output
cdf affy gcrma matchprobes affyio cdf affy gcrma matchprobes affyio
updated 5.3 years ago by 0 • written 17.4 years ago by ★ 2.2k
4
votes
3
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1.1k
views
GCRMA not working inside tryCatch block in R
gcrma simpleaffy error handling trycatch
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
0
votes
1
reply
1.7k
views
Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds while using GCRMA
gcrma wheatcdf cdf
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
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
0
votes
2
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2.5k
views
gcrma error " 'Calloc' could not allocate memory"
gcrma error
updated 6.4 years ago by 65k • written 6.5 years ago by • 0
0
votes
4
replies
2.9k
views
cdf file for Clariom S Human HT
gcrma
6.7 years ago kathleen.klein • 0
2
votes
7
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1.5k
views
Package gcrma: unused argument (validate = FALSE)
gcrma
updated 6.9 years ago by ★ 3.9k • written 6.9 years ago by ▴ 10
2
votes
3
replies
1.4k
views
unusal expression level values after normalization in Affymetrix microarray experiment
microarray gcrma affy hgu133a normalization
updated 7.0 years ago by 50k • written 7.1 years ago by ▴ 50
1
vote
8
replies
7.1k
views
Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 7.1 years ago by 50k • written 16.8 years ago by ▴ 80
0
votes
2
replies
1.1k
views
error in gcrma function
gcrma
updated 7.1 years ago by ★ 3.9k • written 7.1 years ago by • 0
0
votes
1
reply
1.2k
views
single probe represent multiple genes?
gcrma microarray expressionset
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by ▴ 20
0
votes
5
replies
2.1k
views
Problem installing XVector package
software error gcrma Xvector iranges
7.7 years ago • updated 7.6 years ago gary_smith • 0
2
votes
9
replies
3.3k
views
mta10cdf not installed Bioconductor
gcrma
updated 7.7 years ago by ▴ 40 • written 9.4 years ago by • 0
0
votes
2
replies
1.1k
views
GCRMA segmentation fault
gcrma segmentation fault segfault
updated 8.0 years ago by 65k • written 8.0 years ago by • 0
0
votes
0
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1.1k
views
Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
8.4 years ago svlachavas ▴ 830
1
vote
4
replies
1.6k
views
AGI code in gcrma normalization output
gcrma software error annotation
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 40
1
vote
4
replies
1.6k
views
Trouble with gcrma, Segfault on background correction
gcrma affy
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 30
0
votes
1
reply
1.7k
views
Warnings after gcrma normalisation...
Microarray Normalization gcrma Microarray Normalization gcrma
updated 10.0 years ago by 65k • written 10.0 years ago by ▴ 150
1
vote
2
replies
1.8k
views
Help needed: extracting raw intensity values from Affy
probe affy gcrma probe affy gcrma
updated 10.3 years ago by ▴ 20 • written 10.3 years ago by ★ 1.5k
0
votes
0
replies
1.4k
views
How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization hu6800 affy gcrma marray nnNorm Harshlight Microarray hu6800
10.5 years ago Scott Robinson ▴ 130
0
votes
3
replies
7.6k
views
Error: cannot allocate vector of size
gcrma simpleaffy gcrma simpleaffy
updated 10.8 years ago by 65k • written 10.8 years ago by ▴ 50
0
votes
1
reply
1.3k
views
Using gcrma with \"Affymetrix GeneChip miRNA v1.0\" data
miRNA gcrma miRNA gcrma
updated 10.8 years ago by 21k • written 10.8 years ago by ★ 13k
1
vote
4
replies
6.4k
views
How is LIMMA actually calculating the average expression value
probe limma gcrma probe limma gcrma
updated 10.9 years ago by ▴ 150 • written 10.9 years ago by 50k
0
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0
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1.3k
views
How is LIMMA actually calculating the average expression value?
gcrma gcrma
10.9 years ago Garcia Orellana,Miriam ▴ 150
0
votes
7
replies
1.7k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 11.2 years ago by 65k • written 11.2 years ago by ★ 13k
0
votes
2
replies
3.0k
views
R 2.15.2 trouble
affy limma gcrma affy limma gcrma
updated 11.2 years ago by 25k • written 11.2 years ago by ★ 13k
0
votes
3
replies
2.6k
views
[GSVA] Segfault with GSVA
RNASeq Microarray Annotation gcrma convert GSVA RNASeq Microarray Annotation gcrma GSVA
updated 11.3 years ago by ▴ 230 • written 11.3 years ago by ★ 3.2k
0
votes
1
reply
1.2k
views
Can Bioconductor be used offline?
gcrma gcrma
updated 11.3 years ago by ★ 13k • written 11.3 years ago by ▴ 10
0
votes
4
replies
1.5k
views
Affymetrix data double normalisation
Normalization gcrma Normalization gcrma
updated 11.6 years ago by 65k • written 11.6 years ago by ★ 13k
0
votes
5
replies
2.6k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 11.8 years ago by ▴ 930 • written 11.8 years ago by ▴ 150
0
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1
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1.2k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 11.8 years ago by 65k • written 11.8 years ago by ▴ 150
0
votes
0
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1.3k
views
PROBLEM LOADING THE covdesc FILE IN SIMPLEAFFY
Normalization gcrma Normalization gcrma
11.8 years ago Garcia Orellana,Miriam ▴ 150
0
votes
9
replies
2.7k
views
gcrma problem while processing HuGene-1_0-st-v1 genechip from Affymetrix
Normalization gcrma Normalization gcrma
11.9 years ago suparna mitra ▴ 290
0
votes
5
replies
1.7k
views
Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf'
Microarray Normalization cdf gcrma Microarray Normalization cdf gcrma
updated 11.9 years ago by 65k • written 11.9 years ago by ▴ 30
0
votes
3
replies
1.3k
views
Building specific Ortoghonal contrasts in LIMMA
limma gcrma limma gcrma
updated 11.9 years ago by 50k • written 11.9 years ago by ▴ 150
0
votes
2
replies
10.0k
views
problems with "cannot allocate vector of size.."
Microarray gcrma Microarray gcrma
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 70
0
votes
0
replies
1.1k
views
Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!
Cancer cdf probe affy gcrma AnnotationDbi Cancer cdf probe affy gcrma AnnotationDbi
12.1 years ago Benjamin Otto ▴ 830
0
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1
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1.1k
views
arrayQualityMetrics: expression or probe-level data?
Cancer gcrma Cancer gcrma
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 20
0
votes
1
reply
920
views
\'mirna20probe
miRNA affy gcrma miRNA affy gcrma
updated 12.5 years ago by 65k • written 12.5 years ago by ★ 13k
0
votes
2
replies
2.2k
views
Installing packages on R v2.13.2, OSX multiple warning messages
Annotation cdf probe affy gcrma Annotation cdf probe affy gcrma
updated 12.5 years ago by 65k • written 12.5 years ago by ★ 13k
1
vote
1
reply
1.6k
views
gcrma failed on mouse Gene 1.0 ST array
probe gcrma probe gcrma
updated 12.6 years ago by ★ 3.9k • written 12.6 years ago by ▴ 50
0
votes
2
replies
1.6k
views
Unable to read Affy Mouse Exon 1.0 ST array CEL file
Annotation cdf affy gcrma oligo Annotation cdf affy gcrma oligo
updated 12.7 years ago by ★ 3.9k • written 12.7 years ago by ▴ 60
0
votes
1
reply
1.1k
views
gcrma
affy gcrma affy gcrma
updated 12.8 years ago by ▴ 50 • written 12.8 years ago by ▴ 30
0
votes
1
reply
1.1k
views
fold change after gcrma()
gcrma convert gcrma convert
updated 12.9 years ago by ★ 4.3k • written 12.9 years ago by ▴ 40
0
votes
0
replies
871
views
gcrma on affy xlaevis arrays
GO affy gcrma GO affy gcrma
12.9 years ago Tobias Straub ▴ 10
50 results • Page 1 of 1
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Replies
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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