Showing : affyPLM • reset
1
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992
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affyPLM boxplots for subset of samples
affyPLM
updated 7.8 years ago by 65k • written 7.8 years ago by ▴ 360
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1
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2.2k
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Computing NUSE and RLE scores
affyPLM RLE NUSE
updated 9.2 years ago by 21k • written 9.2 years ago by ▴ 10
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0
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1.2k
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affy packages on Linux doesn't get installed
DynDoc tkWidgets affy affyPLM DynDoc tkWidgets affy affyPLM
20.4 years ago juliab@stat.berkeley.edu ▴ 10
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843
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Quantile Normalization on mice data
affyPLM affyPLM
20.2 years ago Yen Lin Chia ▴ 50
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2
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1.1k
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AffyPLM
affyPLM affyPLM
updated 20.2 years ago by ▴ 940 • written 20.2 years ago by ▴ 50
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0
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923
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affyPLM interpretation
affyPLM DOSE affyPLM DOSE
20.2 years ago Arne.Muller@aventis.com ▴ 620
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0
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916
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Quantile Normalization on mice data
Normalization Clustering probe affyPLM Normalization Clustering probe affyPLM
20.2 years ago Arne.Muller@aventis.com ▴ 620
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0
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1.1k
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AffyPLM
affyPLM affyPLM
20.2 years ago Arne.Muller@aventis.com ▴ 620
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0
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1.0k
views
Re: trouble installing "affy" package
Annotation GO Preprocessing Biobase affy affyPLM Annotation GO Preprocessing Biobase
20.1 years ago Debjani Bhowmick ▴ 30
0
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0
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877
views
Interpretation of output of AffyRNAdeg and hist commands
Microarray Regression Cancer affyPLM Microarray Regression Cancer affyPLM
20.0 years ago James W. MacDonald 65k
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0
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638
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using fitPLM weights in limma analysis
affy limma affyPLM affy limma affyPLM
20.0 years ago Tom Price ▴ 20
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1
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1.4k
views
Bioconductor 1.4 released
Proteomics Annotation Normalization GO Cancer CGH pamr gcrma gpls affyPLM webbioc bim
updated 19.9 years ago by ★ 13k • written 20.0 years ago by ▴ 810
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0
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627
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Chip art from affyPLM
affyPLM affyPLM
19.9 years ago Ben Bolstad ★ 1.1k
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0
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617
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Platform independent compiler switches - affyPLM problem
affyPLM affyPLM
19.9 years ago Claudio Lottaz ▴ 110
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1
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1.1k
views
affy package in MacOSX
affy affydata matchprobes affyPLM affy affydata matchprobes affyPLM
updated 19.8 years ago by ▴ 1000 • written 19.8 years ago by ▴ 60
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1
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709
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reference on package affyPLM, fitPLM
affyPLM affyPLM
19.5 years ago Fangxin Hong ▴ 810
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2
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1.3k
views
gregmisc package-problems with BioC latest release?
Biobase annotate edd genefilter geneplotter ROC limma siggenes affyPLM marray Biobase
updated 19.5 years ago by ★ 7.4k • written 19.5 years ago by ▴ 130
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votes
3
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1.2k
views
Install of 1.5 Packages fails
GO edd genefilter annaffy affyPLM marray GO edd genefilter annaffy affyPLM marray
updated 19.5 years ago by ★ 5.5k • written 19.5 years ago by ★ 1.7k
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1
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1.1k
views
Problems with packages: annaffy, GO, KEGG, golubEsets
GO edd annaffy affyPLM GO edd annaffy affyPLM
updated 19.4 years ago by ★ 5.5k • written 19.4 years ago by ▴ 10
0
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0
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914
views
sanity check: recipe for p-value from RMA expression estimates
Normalization probe affy affyPLM Normalization probe affy affyPLM
19.2 years ago Reiner Schulz ▴ 20
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0
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895
views
sanity check: p-value from RMA expression estimates
Normalization probe affy affyPLM Normalization probe affy affyPLM
19.2 years ago Reiner Schulz ▴ 20
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0
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1.0k
views
remove probes - code
cdf probe affy gcrma affyPLM cdf probe affy gcrma affyPLM
19.0 years ago Ariel Chernomoretz ▴ 380
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votes
2
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1.1k
views
Re: how to evaluate the arrays quality?
GO affy affyPLM GO affy affyPLM
updated 18.9 years ago by ▴ 110 • written 18.9 years ago by ▴ 350
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0
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545
views
Re: Use of RMA in increasingly-sized datasets
Microarray affyPLM Microarray affyPLM
18.9 years ago Swati Ranade ▴ 60
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0
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732
views
RMA for bad chips
Microarray Normalization affyPLM Microarray Normalization affyPLM
18.8 years ago James W. MacDonald 65k
0
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3
replies
1.1k
views
AffyPLM
affyPLM affyPLM
18.8 years ago lucia ¿? ▴ 50
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votes
0
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790
views
Error messages in affylmGUI on PC with respect to plotting
Cancer limma affyPLM affylmGUI Cancer limma affyPLM affylmGUI
18.8 years ago Richard Friedman ★ 2.0k
0
votes
3
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902
views
Error messages in affylmGUI on PC with respect to plotting
limma affyPLM affylmGUI limma affyPLM affylmGUI
18.8 years ago Seth Falcon ★ 7.4k
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0
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1.3k
views
NA values
Normalization Cancer limma gcrma affyPLM limmaGUI plier Normalization Cancer limma gcrma
18.8 years ago Brooke-Powell, Elizabeth ▴ 170
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0
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748
views
Limma using all probes on Affy chip
Normalization probe affy limma affyPLM Normalization probe affy limma affyPLM
18.7 years ago Gordon Smyth 50k
0
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6
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1.1k
views
What wrong with my data using LIMMA
Microarray affy limma affyPLM Microarray affy limma affyPLM
updated 18.6 years ago by ★ 1.8k • written 18.6 years ago by 50k
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3
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1.2k
views
LIMMA No residual using rmaPLM
Preprocessing affyPLM Preprocessing affyPLM
updated 18.6 years ago by 50k • written 18.6 years ago by ▴ 270
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0
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555
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MAplot in affyPLM library
affyPLM affyPLM
18.5 years ago Simon Lin ▴ 270
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0
replies
901
views
missing function in duplicateCorrelation?
Biobase affy affydata limma affyPLM Biobase affy affydata limma affyPLM
18.4 years ago Jenny Drnevich ★ 2.2k
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1
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1.1k
views
RNA degradation problem
Normalization affy limma affyPLM PROcess Normalization affy limma affyPLM PROcess
updated 18.3 years ago by ▴ 810 • written 18.3 years ago by ▴ 940
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8
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1.9k
views
Biological replication (was RNA degradation problem)
Normalization probe affy affyPLM Normalization probe affy affyPLM
18.3 years ago Naomi Altman ★ 6.0k
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0
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882
views
Why mm's changing after bg.adjust.gcrma?
drosgenome1 cdf Biobase reposTools affy gcrma affyPLM simpleaffy affyQCReport affyio cdf
17.9 years ago Jenny Drnevich ★ 2.2k
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0
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509
views
Sam always wants more observations
probe Biobase affy affyPLM probe Biobase affy affyPLM
18.0 years ago Charles Crane ▴ 30
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0
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787
views
affyPLM QC
affy affyPLM affy affyPLM
18.0 years ago Tan, Ruimin ▴ 50
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0
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731
views
affyPLM QC Assessment problem
affy affyPLM affy affyPLM
18.0 years ago Tan, Ruimin ▴ 50
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2
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1.3k
views
Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1
affy gcrma matchprobes affyPLM affyio affy gcrma matchprobes affyPLM affyio
updated 17.9 years ago by ▴ 50 • written 17.9 years ago by ▴ 20
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2
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1.1k
views
median of the NUSE value
cdf affy gcrma affyPLM affyio cdf affy gcrma affyPLM affyio
updated 17.9 years ago by ★ 1.2k • written 17.9 years ago by ▴ 270
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1
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1.3k
views
[R] problem loading affycoretools - solved!
Biobase Ruuid genefilter multtest graph limma gcrma matchprobes affyPLM RBGL simpleaffy
updated 17.7 years ago by ★ 7.4k • written 17.7 years ago by ★ 2.2k
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1
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875
views
qc
Survival Biobase genefilter affy affydata affyPLM simpleaffy affyio Survival Biobase
updated 17.7 years ago by 65k • written 17.7 years ago by ▴ 10
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2
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874
views
loading affyPLM with R 2.4.
affyPLM affyPLM
updated 17.7 years ago by ★ 1.2k • written 17.7 years ago by ▴ 20
0
votes
0
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933
views
4 replicates, of 3 tissues- one good hyb (2xreps), one bad hyb (2xreps). Best way forward?
qPCR affy affydata vsn limma gcrma matchprobes affyPLM affyio BRAIN qPCR affy affydata
17.6 years ago k. brand ▴ 420
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0
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959
views
method for removing consistent technical bias?
affy affydata vsn limma gcrma matchprobes affyPLM affyio affy affydata vsn limma gcrma
17.6 years ago k. brand ▴ 420
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2
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952
views
normalize.quantiles.robust: how to implement weights for different arrays?
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio
updated 17.6 years ago by ★ 6.5k • written 17.6 years ago by ▴ 420
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2
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1.1k
views
"normalize.quantiles.robust" produces the SAME intensities from different weights?!
Normalization affydata gcrma matchprobes affyPLM affyio Normalization affydata gcrma
updated 17.6 years ago by ★ 1.2k • written 17.6 years ago by ▴ 420
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2
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2.9k
views
Error in function (classes, fdef, mtable)
cdf genefilter reposTools gcrma matchprobes affyPLM simpleaffy affyio cdf genefilter
updated 17.4 years ago by ★ 7.4k • written 17.4 years ago by ▴ 360
50 results • Page 1 of 1
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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…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
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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