User: Matthew McCall

gravatar for Matthew McCall
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760
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Location:
United States
Website:
http://mnmccall.com/
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Last seen:
1 month ago
Joined:
6 years, 9 months ago
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Posts by Matthew McCall

<prev • 94 results • page 1 of 10 • next >
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Answer: A: Processing several GSM from GEO database using Barcode and fRMA
... Hi Diana, The first step is to access the data. The GEOquery package provides a way to do this from within R. Alternatively, you can download the CEL files from GEO yourself and read them into R using the affy package. This will produce an AffyBatch object similar to the AffyBatchExample object you ...
written 5 days ago by Matthew McCall760
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Answer: A: Minimum number of genes to use R package "nondetects"
... You need to have enough genes (and samples) to get a decent estimate of the missing data mechanism. This package is designed for qPCR data (not microarrays). The 3 example data sets included with the package should provide a sense of the size / type of data sets that can be used.  ...
written 3 months ago by Matthew McCall760
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Comment: C: fRMA normalization for Mouse Gene 2.1 ST Array
... As an R novice, I would not recommend undertaking the creation of your own frma vectors. It can be a fairly involved process, especially when you're dealing with a new platform. However, if you decide to proceed, I would start with this paper: http://www.biomedcentral.com/1471-2105/12/369 And then ...
written 5 months ago by Matthew McCall760
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Answer: A: fRMA normalization for Mouse Gene 2.1 ST Array
... Unfortunately, there are not frma vectors made for this platform. You could make your own frma vectors or use a related preprocessing algorithm (e.g. rma). ...
written 5 months ago by Matthew McCall760
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Answer: A: How to normalize mouse gene 1.0st arry using frma?
... Please make sure you have installed the mogene.1.0.st.v1frmavecs package and that you've read in the data using the oligo package. ...
written 5 months ago by Matthew McCall760
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Comment: C: fRMA error - unable to create unique mapping
... Yes, it will work for exon arrays as well. However, you need to use the oligo package (rather than the affy package) to read in the CEL files.  ...
written 6 months ago by Matthew McCall760
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Comment: C: DESeq fitted values using coefficients vs mu
... Great. Thank you! ...
written 10 months ago by Matthew McCall760
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Comment: C: DESeq fitted values using coefficients vs mu
... One related question: is there a way to calculate the fitted values with betaPrior=TRUE using the coefficients and model matrix rather than assays(obj)[["mu"]] and the size factors? ...
written 10 months ago by Matthew McCall760
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Comment: C: DESeq fitted values using coefficients vs mu
... Got it. Thanks! ...
written 10 months ago by Matthew McCall760
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Comment: C: DESeq fitted values using coefficients vs mu
... Thank you for the fast reply. So with betaPrior=FALSE, I still get some sizable differences. obj <- DESeq(obj, betaPrior=FALSE) log2q1 <- log2(t( t( assays(obj)[["mu"]] ) / sizeFactors(obj) )) log2q2 <- coef(obj) %*% t(attr(obj, "modelMatrix")) summary(as.vector(log2q1-log2q2)) Min. 1 ...
written 10 months ago by Matthew McCall760

Latest awards to Matthew McCall

Scholar 22 months ago, created an answer that has been accepted. For A: Strategies for fRMA on custom dataset(s)?
Scholar 2.8 years ago, created an answer that has been accepted. For A: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?
Scholar 2.8 years ago, created an answer that has been accepted. For A: frma vectors for GPL13158 (Affymetrix HT HG-U133+ PM Array Plate)?

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