User: chandlerjd58

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Posts by chandlerjd58

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pd.mogene.2.0st Error Installing in R 3.1.2
... I am trying to read my mogenest2.0 CEL files into R with oligo. But pd.mogene.2.0st appears to not work for my release of R (says it is not available for R 3.1.2). This seems odd to me since pd.mogene.2.0st is listed as part of the Bioconductor 3.0 release (which works in my version of R). Does anyo ...
microarray oligo R bioconductor written 2.8 years ago by chandlerjd580 • updated 2.8 years ago by Marc Carlson7.2k
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Comment: C: Proper way to build phenoData object?
... Personal belief. I'm happy to be corrected if I'm wrong about this. :) Admittedly, the difference between log2 alone and log2+quantile is minimal when I have made direct comparisons, but there is a difference. If it's something the entire field has decided is acceptable then I will defer to you all. ...
written 2.8 years ago by chandlerjd580
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Comment: C: Proper way to build phenoData object?
... Thanks Guido! So I guess head(pheno) could look like: Name Class1 Class2 Class 3 NameA 1 0 0 NameB 0 1 0 NameC 1 0 1 NameD 0 1 1 From there, you use Biobase or affy to make pheno into an ADF which is read into phenoData for MyArrayData.  Do you have a preference to use AffyBatch or Expression ...
written 2.8 years ago by chandlerjd580
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Proper way to build phenoData object?
... Rather than starting at RMA, I'd like to load my Affy data into an expression set in R and use limma to do the full, proper fold change analysis. (My understanding is that RMA is quantile normalized, so fold change analysis won't be accurate.) My goal is to go from CEL files to the limma top table. ...
biobase affy limma written 2.8 years ago by chandlerjd580 • updated 2.8 years ago by Guido Hooiveld2.2k
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Comment: C: Simple significance test functions from R packages limma and plsgenomics
... I think there is some mis-communication. Essentially, I am trying to emulate coding I have seen done previously in my lab. This is an example based on a 7x24,589 feature data matrix (6 samples and an identifier column): design <- model.matrix (~factor (c("Con", "Con", "Con", "Cd", "Cd", "Cd"))) ...
written 2.8 years ago by chandlerjd580
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Comment: C: Simple significance test functions from R packages limma and plsgenomics
... It could just be that I don't understand. I am very new to bioinformatics (biologist by training), but I am trying to understand some of the basics on my own to not have to rely as much waiting on others to do the work for me. One thing that frustrates me about the manual is that it seems to be writ ...
written 2.8 years ago by chandlerjd580
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Comment: C: Simple significance test functions from R packages limma and plsgenomics
... My Affy data is already log2 transformed, but are you suggesting it is conventional to loess normalize the array data as well?  I attempted to place the suggested limma changes into my original code structure. I'm running it now but it seems to be stuck or taking a long time.   #Read in your file ...
written 2.8 years ago by chandlerjd580
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Simple significance test functions from R packages limma and plsgenomics
... I use R in bioinformatic analysis of metabolomics and gene expression data. One of my colleagues wrote a (nearly published) R program to bundle the features of many R packages for informatics, including limma and plsgenomics packages. I have come to rely on the complex program primarily for somethin ...
microarray limma differential gene expression plsgenomics written 2.9 years ago by chandlerjd580 • updated 2.8 years ago by Gordon Smyth32k

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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Simple significance test functions from R packages limma and plsgenomics

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