User: Juliet Hannah

gravatar for Juliet Hannah
Juliet Hannah360
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360
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8 years, 5 months ago
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Posts by Juliet Hannah

<prev • 44 results • page 2 of 5 • next >
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limma roast syntax for overall anova
... All, I am testing an overall anova (4 groups; is there any difference across groups) using the following design matrix in limma (Intercept) B C D 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 0 0 5 1 0 0 0 6 1 0 0 0 I have used ROAST (in limma) ...
limma written 5.1 years ago by Juliet Hannah360 • updated 4.8 years ago by Gordon Smyth38k
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Comment: C: GWAS with family data
... The kinship2 package implements a mixed model for family data. It is not GWAS specific, but has been used in GWAS studies with family data. On Wed, Apr 16, 2014 at 3:00 PM, NAOMI S ALTMAN wrote: > Thanks, Stephanie. > > This was actually to demonstrate GWAS to my course. The only GWAS ...
written 5.3 years ago by Juliet Hannah360
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Comment: C: help with SCAN.UPC and u133aaofav2
... Hi Steve, Thanks for responding. I am using the cmap data, which I believe was used in your SCAN paper. Did you you the three types of chips? Thanks, Juliet On Fri, Nov 1, 2013 at 10:53 AM, Steve Piccolo wrote: > Hi Juliet, > > Thanks for your question. > > You can get around ...
written 5.8 years ago by Juliet Hannah360
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help with SCAN.UPC and u133aaofav2
... All, I am trying to run scan and I obtain the following error. I searched for the packages (pd.u133aaofav2), could not find them, and I'm confused about how to proceed: # command used normalized = SCAN("myCEL.CEL") # error message Loading required package: pd.u133aaofav2 Attempting to obtain ' ...
annotation written 5.8 years ago by Juliet Hannah360 • updated 5.8 years ago by Stephen Piccolo560
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Comment: C: enrichment packages that accept t-stat (or related stat) as input
... Hi Robert, Thanks for your response. I will look into it. Also is it correct GSVA always requires an expression matrix. It seems that it integrates with limma, so if I have done an analysis in limma does this mean that I should be able to use GSVA for an enrichment analysis. Thanks, Juliet ...
written 6.0 years ago by Juliet Hannah360 • updated 4.8 years ago by Gordon Smyth38k
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Comment: C: enrichment packages that accept t-stat (or related stat) as input
... Hi Guido, Thanks for your response. Yes, I should have used the 'pre-ranked' descriptor. I am looking for a Bioconductor implementation. It seems that in the places I've looked (gsealm, GSVA, Graphite), an expression matrix must be provided (or I missed the other options). Regards, Juliet ...
written 6.0 years ago by Juliet Hannah360 • updated 4.8 years ago by Gordon Smyth38k
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enrichment packages that accept t-stat (or related stat) as input
... All, I am looking for an Bioconductor enrichment package that does something similar to GSEA for pre-computed test statistics. This method would not rely on a cutoff. That is, rather than passing an expression matrix, one can compute summarizes outside of the package (such as a limma t), and then p ...
limma written 6.0 years ago by Juliet Hannah360 • updated 4.8 years ago by Gordon Smyth38k
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Comment: C: combining/merging several ExpressionSet objects from SCAN
... Thanks Tim. I'm trying this out and looks like I did not think this through. So let's say I have several CEL files. I am spreading this out over a cluster. So I have myFiles = ("cel1.CEL","cel2,CEL") # pick one file fileToNormalize = myFiles[fileIndex] # normalize this to create eset normaliz ...
written 6.0 years ago by Juliet Hannah360
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Comment: C: combining/merging several ExpressionSet objects from SCAN
... Thanks Ryan. I'll try this out. What if the esets are already generated. So I have a bunch laying around. I'll look into your answer more and see if I can apply it to this situation. On Fri, Aug 9, 2013 at 3:14 PM, Ryan C. Thompson wrote: > celfiles <- list.files(pattern=".*\\.CEL$"**) & ...
written 6.0 years ago by Juliet Hannah360
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combining/merging several ExpressionSet objects from SCAN
... All, SCAN outputs an ExpressionSet object for each CEL file. What is a nicer way to put them all into a matrix other than converting each one to a vector and then cbinding after each conversion? Thanks, Juliet [[alternative HTML version deleted]] ...
written 6.0 years ago by Juliet Hannah360 • updated 6.0 years ago by W. Evan Johnson800

Latest awards to Juliet Hannah

Popular Question 2.7 years ago, created a question with more than 1,000 views. For unable to install lumi package
Popular Question 2.7 years ago, created a question with more than 1,000 views. For help with SCAN.UPC and u133aaofav2
Popular Question 2.7 years ago, created a question with more than 1,000 views. For limma roast syntax for overall anova
Popular Question 2.7 years ago, created a question with more than 1,000 views. For limma roast syntax and interpretation
Popular Question 2.7 years ago, created a question with more than 1,000 views. For problems installing xcms package
Popular Question 2.7 years ago, created a question with more than 1,000 views. For limma roast syntax and interpretation

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