User: Yolande Tra

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Yolande Tra160
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Posts by Yolande Tra

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Answer: A: Gostats with Yeast annotation
... Hi Marc, Thank you for the info. If I want to do a gene set enrichment analysis using KEGG, do I need the other version that has entrez gene ID. If yes, would you point to me the link to find this version of the package. Thanks again. Yolande ________________________________ From: Marc Carlson [ ...
written 10.5 years ago by Yolande Tra160
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Gostats with Yeast annotation
... Hi Alex, I need some help. For yeast with two-color microarray, do you know which identifier to use (there is no org.Sc.sgdENTREZID)in the ls("package:org.Sc.sgd) [1] "org.Sc.sgd" "org.Sc.sgd_dbconn" "org.Sc.sgd_dbfile" "org.Sc.sgd_dbInfo" [5] "org.Sc.sgd_dbschema" "org.Sc.sgdALIAS" ...
microarray annotation go cancer yeast gostats written 10.5 years ago by Yolande Tra160
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Answer: A: Limma: design matrix
... Thank you for the insight. Yolande -----Original Message----- From: Naomi Altman [mailto:naomi@stat.psu.edu] Sent: Mon 1/26/2009 9:53 PM To: Yolande Tra; Naomi Altman; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Limma: design matrix I guess the question is how stringently you want to do t ...
written 10.6 years ago by Yolande Tra160
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Answer: A: Limma: design matrix
... Hi Naomi, Thank you for your reply. Would you say then we should test for batch effect and slide effect using the command lm and a formula with main effect and interaction or we can just use a design matrix where each array is considered as a biological replicate. Looking forward to your insight. ...
written 10.6 years ago by Yolande Tra160
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Limma: design matrix
... Hi all, I have an unusual microarray design. The experiment is meant to compare two conditions. We have 4 slides of microarrays: all four considered as biological replicates. However, one slide contains 2 replicate arrays (we named top and bottom). These two come from the same culture. The design ...
microarray limma written 10.6 years ago by Yolande Tra160
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limma and duplicate correlation
... Dear List, I am working on yeast data that has 11 positive controls replicated 17 times. They are irregularly located in the array. After obtaining MA object, I could order the genes and get them next to each other. My question is, how would I incorporate the duplicate correlation aspect when defin ...
yeast written 11.1 years ago by Yolande Tra160 • updated 11.1 years ago by Mark Cowley910
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creating expression set
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written 11.7 years ago by Yolande Tra160
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Answer: A: creating expression set
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written 11.8 years ago by Yolande Tra160
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creating expression set
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written 11.8 years ago by Yolande Tra160 • updated 11.8 years ago by Martin Morgan ♦♦ 23k
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Answer: A: How to do clustering
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written 12.2 years ago by Yolande Tra160

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