Showing : gcrma • reset
2
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3
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875
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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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854
views
u133aaofav2 platform gcrma Normalization
u133aaofav2 annotation gcrma
4.8 years ago samane.khoshbakht • 0
0
votes
1
reply
611
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 5.6 years ago by 65k • written 5.6 years ago by • 0
0
votes
1
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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 5.7 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 6.5 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
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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
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
2.2k
views
Problem installing XVector package
software error gcrma Xvector iranges
7.7 years ago gary_smith • 0
2
votes
9
replies
3.3k
views
mta10cdf not installed Bioconductor
gcrma
updated 7.8 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
replies
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
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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
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1.7k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 11.2 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
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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 11.9 years ago by ▴ 930 • written 11.9 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 11.9 years ago by 65k • written 11.9 years ago by ▴ 150
0
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0
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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
10.0k
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
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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
923
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
873
views
gcrma on affy xlaevis arrays
GO affy gcrma GO affy gcrma
13.0 years ago Tobias Straub ▴ 10
50 results • Page 1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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