User: Elisabetta Manduchi

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Posts by Elisabetta Manduchi

<prev • 16 results • page 1 of 2 • next >
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DiffBind error with DBA_DESEQ_GLM and warning with DBA_EDGE_GLM
... Hello, I'm using DiffBind version 1.2.0 with R 2.15.0 on linux. I've created a dba object data.deseq and run: > data.deseq = dba.count(data.deseq,score=DBA_SCORE_TMM_READS_EFFECTIVE,bRemoveDuplic ates=T,bCorPlot=F) > data.deseq = dba.contrast(data.deseq,categories=DBA_TISSUE,block=DBA_FACTO ...
a4 diffbind written 7.4 years ago by Elisabetta Manduchi160
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error with MEDIPS.CpGenrich when using extend
... Hello, I'm using MEDIPS version 1.20.0 on R version 2.13.2 with a Sus scrofa 2 BSgenome package that I've built according to instructions. I can run the MEDIPS.CpGenrich function in default mode (i.e. without setting a value for extend) on my set. But, if I try to provide a value for the extend p ...
medips written 8.1 years ago by Elisabetta Manduchi160 • updated 8.1 years ago by Joern Dietrich10
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Comment: C: (BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem
... Thanks for the response. I guess I hadn't fully understood this seed file field. I've now set it to 4 (since I have gap.txt, plus chromosomal RM, TRF files and no since files are needed for AMB masks) and the function is running now. Elisabetta --- On Mon, 10 Oct 2011, Hervé Pagès wrote: > Hi ...
written 8.2 years ago by Elisabetta Manduchi160
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(BSgenome) forgeBSgenomeDataPkg for Sus scrofa problem
... Hello, I'm trying to build a data package for Sus scrofa with BSgenome (R version 2.13.2 and BSgenome version 1.20.0). At the bottom of this email I've copied my seed file. I've downloaded the sequence files from UCSC and checked the md5sums. I've also downloaded the gap.txt and masks files (chr*. ...
sus scrofa bsgenome written 8.2 years ago by Elisabetta Manduchi160 • updated 8.2 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: problems with gcrma just.gcrma
... Jim, > Hi Elisabetta, > > I see your problem now. First, you are using just.gcrma() rather than > justGCRMA(), which is the function you should be using. The problem here > is that you are passing an argument 'samepleNames' to just.gcrma() which > a.) doesn't exist for this funct ...
written 13.0 years ago by Elisabetta Manduchi160
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Answer: A: problems with gcrma just.gcrma
... Hi Seth, thanks for the futher suggestions. In response, first, the output of sessionInfo() is: --- R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_Un ...
written 13.0 years ago by Elisabetta Manduchi160
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Comment: C: problems with gcrma just.gcrma
... Hi Jim, thanks for your feedback. They appear to be all .CEL files: > cel.files [1] "../../data_repository/quantifications/NDminus_E15.5_Pan_11-13-03_MGU7 4Av2.CEL" [2] "../../data_repository/quantifications/NDminus_E18_Pan_MGU74Av2.CEL" [3] "../../data_repository/quantifications/NDminus_ ...
written 13.0 years ago by Elisabetta Manduchi160
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problems with gcrma just.gcrma
... Hello, I'm trying to use just.gcrma with data from Affy MGU74Av2 and am getting the error at the bottom of what's copied below re read.probematrix. I'm running version 2.4.0 of R and gcrma version 2.6.0. The mgu74av2 packages being downloaded are version 1.14.0. Can anybody advice on what I can do ...
mgu74av2 affy gcrma written 13.0 years ago by Elisabetta Manduchi160
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AnnBuilder: sourceURLs not found error
... Hello, I'm running R 1.9.1 on Windows 2000 and tried to test some of the code in the AnnBuilder (1.4.2) package from the vignette. I'm encountering an error, which I'm not clear on how to fix. Code and error are copied below. Note that I've tried to run the same code on Linux (R version 1.9.0) and ...
annbuilder process written 15.3 years ago by Elisabetta Manduchi160 • updated 15.3 years ago by John Zhang2.9k
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Answer: A: MvA plot
... Martino, typically M=log(R)-log(G) and A=(log(R)+log(G))/2 where logs are base 2 and R is the red channel intensity and G the green channel one (after possible background correction). Elisabetta On Tue, 17 Feb 2004, Martino Barenco wrote: > Just a simple question: what does the "M" in MvA sta ...
written 15.8 years ago by Elisabetta Manduchi160

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