Showing : gcrma • reset
2
votes
3
replies
888
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
2
replies
861
views
u133aaofav2 platform gcrma Normalization
u133aaofav2 annotation gcrma
4.9 years ago samane.khoshbakht • 0
0
votes
1
reply
619
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
1.3k
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
4
votes
3
replies
1.1k
views
GCRMA not working inside tryCatch block in R
gcrma simpleaffy error handling trycatch
updated 5.6 years ago by 65k • written 5.6 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 5.7 years ago by 65k • written 5.7 years ago by • 0
0
votes
2
replies
2.5k
views
gcrma error " 'Calloc' could not allocate memory"
gcrma error
updated 6.5 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
replies
1.6k
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 7.1 years ago by 50k • written 7.1 years ago by ▴ 50
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
2.2k
views
Problem installing XVector package
software error gcrma Xvector iranges
7.7 years ago gary_smith • 0
0
votes
2
replies
1.1k
views
GCRMA segmentation fault
gcrma segmentation fault segfault
updated 8.1 years ago by 65k • written 8.1 years ago by • 0
0
votes
0
replies
1.1k
views
Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
8.5 years ago svlachavas ▴ 830
1
vote
4
replies
1.6k
views
AGI code in gcrma normalization output
gcrma software error annotation
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 40
2
votes
9
replies
3.3k
views
mta10cdf not installed Bioconductor
gcrma
updated 7.8 years ago by ▴ 40 • written 9.5 years ago by • 0
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
0
votes
8
replies
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
1
vote
2
replies
1.9k
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
10.6 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
6.5k
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
votes
0
replies
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 11.3 years ago by 65k • written 11.3 years ago by ★ 13k
0
votes
2
replies
3.0k
views
R 2.15.2 trouble
affy limma gcrma affy limma gcrma
updated 11.3 years ago by 25k • written 11.3 years ago by ★ 13k
0
votes
3
replies
2.7k
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 ★ 3.3k
0
votes
1
reply
1.2k
views
Can Bioconductor be used offline?
gcrma gcrma
updated 11.4 years ago by ★ 13k • written 11.4 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
1
reply
1.2k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 11.9 years ago by 65k • written 11.9 years ago by ▴ 150
0
votes
5
replies
2.6k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 11.9 years ago by ▴ 930 • written 11.9 years ago by ▴ 150
0
votes
0
replies
1.3k
views
PROBLEM LOADING THE covdesc FILE IN SIMPLEAFFY
Normalization gcrma Normalization gcrma
11.9 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 12.0 years ago by 50k • written 12.0 years ago by ▴ 150
0
votes
2
replies
10k
views
problems with "cannot allocate vector of size.."
Microarray gcrma Microarray gcrma
updated 12.2 years ago by ★ 13k • written 12.2 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
12.2 years ago Benjamin Otto ▴ 830
0
votes
1
reply
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
928
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 12.6 years ago by 65k • written 12.6 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
875
views
gcrma on affy xlaevis arrays
GO affy gcrma GO affy gcrma
13.0 years ago Tobias Straub ▴ 10
0
votes
3
replies
1.2k
views
Problem using justGCRMA
gcrma gcrma
updated 13.0 years ago by 65k • written 13.0 years ago by ▴ 10
0
votes
1
reply
909
views
customCDF name not recognized and switched to Affy CDF
cdf affy gcrma cdf affy gcrma
updated 13.1 years ago by 65k • written 13.1 years ago by ▴ 80
50 results • Page 1 of 1
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
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Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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