Showing : plier • reset
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what normalization method does mas5 use
Normalization GO affy gcrma plier Normalization GO affy gcrma plier
updated 19.8 years ago by ▴ 100 • written 19.8 years ago by ▴ 10
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8
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1.8k
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error message in gcrma
cdf affy gcrma matchprobes plier cdf affy gcrma matchprobes plier
updated 17.9 years ago by ★ 7.4k • written 17.9 years ago by ▴ 520
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2
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results of justPlier vs. RMA
Clustering affy plier affyio Clustering affy plier affyio
updated 17.4 years ago by ▴ 120 • written 17.4 years ago by ▴ 360
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5
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1.4k
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PLIER affinities redux
cdf probe Biobase affy plier cdf probe Biobase affy plier
updated 18.5 years ago by ★ 1.1k • written 18.5 years ago by ▴ 60
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6
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1.4k
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Affy EXON Array: iterPLIER or RMA
Cancer plier Cancer plier
updated 17.0 years ago by 65k • written 17.0 years ago by ★ 1.9k
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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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4
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1.3k
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problems rma() with mouse exon affy data in exonmap package
Survival cdf genefilter affy simpleaffy plier exonmap Survival cdf genefilter affy
updated 16.6 years ago by 65k • written 16.6 years ago by ▴ 20
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1
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1.3k
views
Prokaryotic_Rhodobacter capsulatus GEP
Epigenetics cdf affy makecdfenv plier affxparser preprocessCore Epigenetics cdf affy
updated 15.4 years ago by ▴ 140 • written 15.4 years ago by 65k
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3
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1.2k
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RMA, d-chip and Plier for new chip type Human/Mouse/Rat Gene
plier plier
updated 16.2 years ago by ★ 2.4k • written 16.2 years ago by ▴ 30
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1
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1.2k
views
annaffy errors
GO Survival mgu74av2 cdf annotate affy limma gcrma matchprobes annaffy simpleaffy plier
updated 17.2 years ago by 65k • written 17.2 years ago by ▴ 320
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1.1k
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Normalization Recommendations- severe biological variation (from the digest)
Normalization vsn plier Normalization vsn plier
updated 15.8 years ago by ★ 6.0k • written 15.8 years ago by ▴ 20
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0
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median polish vs mas/PLIER info
Microarray Normalization Cancer probe affy GeneSpring PROcess plier Microarray Cancer
19.9 years ago Anthony Bosco ▴ 500
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1
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1.1k
views
No changes between Groups using GeneST Arrays from Affymetrix
GO vsn plier GO vsn plier
updated 14.0 years ago by ▴ 230 • written 14.0 years ago by ▴ 830
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1
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1.1k
views
Exonmap mapping problems
Survival genefilter affy plier affyio exonmap Survival genefilter affy plier affyio
updated 16.6 years ago by ▴ 120 • written 16.7 years ago by ▴ 10
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3
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1.1k
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Anyone get plier to install on OS X?
plier plier
18.9 years ago • updated 18.8 years ago Ken Termiso ▴ 250
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2
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1.1k
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plier error
plier plier
updated 17.6 years ago by ★ 1.1k • written 17.7 years ago by ▴ 360
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1
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1.1k
views
PLIER is available as open source
plier SANTA plier SANTA
updated 19.5 years ago by ▴ 50 • written 19.5 years ago by ▴ 50
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0
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FARMS package (fwd)
Microarray Normalization cdf plier farms Microarray Normalization cdf plier farms
11.7 years ago Günter Klambauer ▴ 540
0
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1
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1.0k
views
PLIER Error
plier plier
updated 19.2 years ago by ★ 1.1k • written 19.2 years ago by ▴ 500
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2
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1.0k
views
Prokaryotic_Rhodobacter capsulatus GEP
cdf plier cdf plier
updated 15.4 years ago by 25k • written 15.4 years ago by ▴ 140
0
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2
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970
views
Running justRMA on .CEL files in another directory
plier plier
updated 19.9 years ago by ▴ 70 • written 19.9 years ago by ▴ 50
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0
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956
views
Affymetrix gene st array - ok to do statistics on Category:Main only?
limma plier oligo limma plier oligo
11.7 years ago Martin O'Hare ▴ 10
0
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2
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955
views
PLIER: two questions
plier plier
updated 18.8 years ago by ★ 1.8k • written 18.8 years ago by ▴ 380
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3
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953
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Standard error in summarization ExpressionSets
plier plier
updated 15.9 years ago by 65k • written 15.9 years ago by ▴ 10
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941
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problem with function to interrogate x:Map (exonmap)
Survival genefilter affy plier affyio exonmap Survival genefilter affy plier affyio
16.6 years ago Wolfgang Raffelsberger ▴ 160
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0
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Question regarding bg correction/normalization/summarization
Normalization Cancer probe affy vsn plier Normalization Cancer probe affy vsn plier
19.8 years ago Wolfgang Huber ★ 13k
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1
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906
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AFFY PLIER ALGORITHM
plier plier
20.0 years ago Anthony Bosco ▴ 500
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2
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Affy PLIER
plier plier
updated 19.5 years ago by ★ 2.3k • written 19.5 years ago by ★ 1.4k
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1
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876
views
PLIER affinities
rae230a cdf probe reposTools affy plier rae230a cdf probe reposTools affy plier
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 80
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1
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861
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plier crashes with 51 CEL files
gcrma PROcess plier gcrma PROcess plier
19.1 years ago Adaikalavan Ramasamy ★ 1.8k
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1
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859
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Mismatch probe handling for exon arrays
Cancer Breast probe affy plier Cancer Breast probe affy plier
updated 17.5 years ago by 65k • written 17.5 years ago by ▴ 310
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853
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PLIER affinities redux
ath1121501 cdf probe Biobase affy plier ath1121501 cdf probe Biobase affy plier
18.5 years ago Matthew Hannah ▴ 940
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0
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plier using reference set normalization
Normalization plier RefPlus Normalization plier RefPlus
16.1 years ago Roumyana Yordanova ▴ 110
0
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0
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814
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questions on BioC's implementation of plier
Normalization plier Normalization plier
17.3 years ago Jenny Drnevich ★ 2.2k
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808
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PLIER
plier plier
19.2 years ago Crispin Miller ★ 1.1k
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MAS5+32, PLIER+16 alorithms reported in affycomp
Normalization probe affycomp plier Normalization probe affycomp plier
19.2 years ago Ariel Chernomoretz ▴ 380
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0
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778
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XPS package working with Affymetrix GeneChip 1.0 ST at gene level
cdf affy plier xps cdf affy plier xps
11.9 years ago cstrato ★ 3.9k
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2
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766
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Affymetrix question
plier plier
updated 18.5 years ago by 65k • written 18.5 years ago by ▴ 50
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760
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justPlier() on UNIX
plier plier
16.9 years ago Pickard, Mike ▴ 10
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0
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754
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plier package
Normalization cdf plier Normalization cdf plier
11.8 years ago fire1976 wyoming ▴ 380
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1
reply
749
views
Problems with justGCRMA: Error in bg.adjust.fullmodel
vsn gcrma matchprobes plier vsn gcrma matchprobes plier
updated 18.6 years ago by 65k • written 18.7 years ago by ▴ 350
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1
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741
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PLIER -- low values?
Microarray plier Microarray plier
updated 18.9 years ago by 65k • written 18.9 years ago by ▴ 190
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0
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704
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help with justPlier
plier plier
17.7 years ago He, Yiwen NIH/CIT ▴ 360
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0
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637
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Re:PLIER wierd Mvs A
plier plier
19.2 years ago Anthony Bosco ▴ 20
44 results • Page 1 of 1
Recent ...
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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