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pamr
•
reset
0
votes
0
replies
919
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
5.6 years ago
jmsendoya
• 0
0
votes
1
reply
1.0k
views
pamr
pamr
pamr
updated 11.4 years ago by
James W. MacDonald
65k • written 11.4 years ago by
mbranham@fcm.uncu.edu.ar
▴ 10
0
votes
2
replies
1.2k
views
pam implementation
pamr
pamr
updated 11.5 years ago by
John Lande
▴ 280 • written 11.5 years ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
1.4k
views
a bug in the function pamr.plotcen()
pamr
pamr
updated 12.9 years ago by
Martin Morgan
25k • written 12.9 years ago by
Alogmail2@aol.com
▴ 90
0
votes
1
reply
1.8k
views
Error in pamr.predict
pamr
pamr
updated 15.0 years ago by
Hervé Pagès
16k • written 15.0 years ago by
Richard Yanicky
▴ 10
0
votes
4
replies
1.1k
views
problem regarding runtime of pamr.cv
pamr
pamr
updated 15.2 years ago by
James W. MacDonald
65k • written 15.2 years ago by
ALok
▴ 170
0
votes
0
replies
936
views
question about pamr.listgenes ....
pamr
pamr
15.7 years ago
ALok
▴ 170
0
votes
0
replies
1.1k
views
pamr.cv function
Cancer
pamr
Cancer
pamr
16.2 years ago
Patricia Greninger
▴ 10
0
votes
1
reply
1.2k
views
problem with pamr.listgenes in pamr package
pamr
pamr
updated 17.0 years ago by
Giovanni Coppola
▴ 250 • written 17.0 years ago by
Alice LE BARS
▴ 10
0
votes
1
reply
1.4k
views
Error of pamr.knnimpute
Microarray
pamr
Microarray
pamr
updated 17.3 years ago by
James W. MacDonald
65k • written 17.3 years ago by
washiot+1@gmail.com
▴ 10
0
votes
1
reply
841
views
magnifying genenames in pamr.plotcen()
pamr
pamr
updated 18.1 years ago by
James W. MacDonald
65k • written 18.1 years ago by
Benjamin Otto
▴ 830
0
votes
0
replies
932
views
pamr package - problem with pamr.cv() function
pamr
pamr
18.1 years ago
Vincent Negre
▴ 30
0
votes
3
replies
1.2k
views
How to write a text file of a pamr.confusion table ?
pamr
pamr
updated 18.4 years ago by
Björn Usadel
▴ 250 • written 18.4 years ago by
Giulio Di Giovanni
▴ 540
0
votes
1
reply
1.0k
views
pamr and samr problems with windowsXP - pop-up windows
pamr
pamr
updated 18.6 years ago by
Seth Falcon
★ 7.4k • written 18.6 years ago by
Giulio Di Giovanni
▴ 540
0
votes
3
replies
1.1k
views
pamr, samr and RWinEdt conficts - New editor req info
pamr
pamr
updated 18.6 years ago by
Seth Falcon
★ 7.4k • written 18.6 years ago by
Giulio Di Giovanni
▴ 540
0
votes
0
replies
967
views
Re: Re: segmentation error in pamr.knnimpute
pamr
impute
pamr
impute
19.0 years ago
Alice Le Bars
▴ 40
0
votes
1
reply
822
views
segmentation error in pamr.knnimpute
pamr
pamr
updated 19.0 years ago by
Seth Falcon
★ 7.4k • written 19.0 years ago by
Alice Le Bars
▴ 40
0
votes
2
replies
1.5k
views
pamr / R graphics recording
pamr
pamr
updated 19.3 years ago by
Min-Han Tan
▴ 40 • written 19.3 years ago by
Katleen De Preter
▴ 130
0
votes
2
replies
1.7k
views
Installation Problem on OS X
GO
geneplotter
graph
Rgraphviz
pamr
globaltest
GO
geneplotter
graph
Rgraphviz
pamr
updated 19.4 years ago by
Marcus Davy
▴ 680 • written 19.4 years ago by
David Rocke
▴ 10
0
votes
1
reply
1.0k
views
Application of PAMR from Affy to spot data
affy
pamr
affy
pamr
updated 19.6 years ago by
rgentleman
★ 5.5k • written 19.6 years ago by
Tan, MinHan
▴ 180
0
votes
6
replies
1.5k
views
pamr Error: each class must have >1 sample
GO
pamr
GO
pamr
updated 19.8 years ago by
Kasper Daniel Hansen
▴ 630 • written 19.8 years ago by
Dick Beyer
★ 1.4k
0
votes
0
replies
752
views
pamr and sample.subset option
pamr
pamr
19.8 years ago
Dr Gyorffy Balazs
▴ 320
0
votes
2
replies
1.2k
views
Hierarchical clustering and shrinking centroids...
Classification
Clustering
pamr
Classification
Clustering
pamr
updated 19.9 years ago by
Stephen Henderson
★ 1.0k • written 19.9 years ago by
Tan, MinHan
▴ 180
0
votes
0
replies
1.2k
views
Problem with PAM using R 1.9.0
pamr
pamr
19.9 years ago
Michelle Kittleson
▴ 10
0
votes
1
reply
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
Wolfgang Huber
★ 13k • written 20.0 years ago by
A.J. Rossini
▴ 810
0
votes
1
reply
1.2k
views
Bug with R 1.9.0 beta (3/23) and PAMR?
pamr
pamr
updated 20.1 years ago by
Liaw, Andy
▴ 360 • written 20.1 years ago by
Tan, MinHan
▴ 180
0
votes
0
replies
877
views
wee query on pamr.knnimpute
pamr
pamr
20.2 years ago
Aedin Culhane
▴ 310
27 results • Page
1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
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…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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Chris
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