User: Ninni Nahm

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Ninni Nahm50
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Germany
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2 years, 10 months ago
Joined:
3 years, 10 months ago
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n********@gmail.com

Posts by Ninni Nahm

<prev • 7 results • page 1 of 1 • next >
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Comment: A: Voom without design matrix
... Hi!  Thank you! I want to use elastic net with the output. My plan was to use the fpkm table with voom and then apply elastic net. Nina ...
written 2.8 years ago by Ninni Nahm50
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Voom without design matrix
... Hi all! I have some RNA-seq data with only one phenotype (disease)  and no controls. I want to use voom to 'convert' the data to 'microarray' like data. Is this possible?  I do not want to do a differential expression analysis.  Best  Nina ...
limma voom written 2.8 years ago by Ninni Nahm50
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Comment: C: no method for coercing S4 class to a vector
... Thank you! That did the trick! On Fri, Sep 12, 2014 at 2:45 PM, Andrzej Ole? wrote: > Dear Ninni, > > you probably need to import the 'as.data.frame' method for GRanges > objects in your NAMESPACE file: > > importMethodsFrom(GenomicRanges, as.data.frame) > > > Cheers, & ...
written 3.2 years ago by Ninni Nahm50
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Comment: C: design matrix paired data
... Hi Bernd! Thanks again for your help! Maybe you did not see it, but I have this line here: colnames(design) <- c("intercept", "patient1", "patient2", "treatment") to rename the column names, so the tt <- topTable(fitNoAdj, coef= "treatment", adjust="fdr") command should work :) (unless I ...
written 3.5 years ago by Ninni Nahm50
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Comment: C: How to do Affy ST array analysis
... Thank you, Bernd! and of course Jim!! :) On Wed, May 7, 2014 at 6:22 PM, Bernd Klaus wrote: > Hi Ninni, > > no, you need to switch, there is an annotation data base for every single > platform (thanks to Jim MacDonald!), search here: > > http://bioconductor.org/packages/releas ...
written 3.5 years ago by Ninni Nahm50
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Comment: C: How to do Affy ST array analysis
... Thank you! That was very very helpful! I wanted to ask if I can use the hugene20sttranscriptcluster.db package for all hugene arrays? I have one more to analyze, which is a st 1 array. Best Ninni On Wed, May 7, 2014 at 2:57 PM, Bernd Klaus wrote: > Hi Ninni, > > I guess a very simple w ...
written 3.5 years ago by Ninni Nahm50
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Comment: C: conditional merge of duplicated rows in data.frame
... Thank you! Works perfectly! I did not know about the split function -Ninni On Mon, Jan 20, 2014 at 9:03 PM, Martin Morgan wrote: > On 01/20/2014 08:54 AM, Ninni Nahm [guest] wrote: > >> >> Hi all! >> >> I have the following problem. >> >> chr13 1260 ...
written 3.8 years ago by Ninni Nahm50

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