User: PyPer

gravatar for PyPer
PyPer20
Reputation:
20
Status:
New User
Location:
Australia
Last seen:
4 years, 5 months ago
Joined:
4 years, 6 months ago
Email:
j*******@uni.sydney.edu.au

Posts by PyPer

<prev • 8 results • page 1 of 1 • next >
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Determining and separating Affy Chips from GEOquery?
... I am currently utilizing a dataset GSE14520 from the GEO website. I understand that it utilizes two chips U133A and U133A 2.0. For preliminary analysis I only need to utilize U133A. Is there an easy way to sort the cel files into their appropriate platform? or do i have to write a script to do it? ...
affy geoquery written 4.4 years ago by PyPer20 • updated 4.4 years ago by James W. MacDonald49k
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Processing RAW CEL files from GEO
... Does anyone have any good resource that will provide a vignette and step by step example of how to process RAW files from GEO? I understand that you utilize getGEOSuppFiles, untar and then readaffy() What I don't get is why there are exp files that are zipped with the cel files. How do I utilize t ...
geoquery cel raw readaffy written 4.5 years ago by PyPer20 • updated 4.5 years ago by Sean Davis21k
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Comment: C: Normalizing Expressionset Exprs without Raw CEL files
... So say for example i'm working on a breast cancer set from GEO GSE5764. I run the usual code to grab it; gse <- getGEO("GSE5764", GSEMatrix=TRUE) Then I attempt to normalize it. t1 <- UFC_Generic_ExpressionSet(gse) and then i visualize it simply by boxplot(exprs(t1)) and what you see is th ...
written 4.5 years ago by PyPer20
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Comment: C: Normalizing Expressionset Exprs without Raw CEL files
... I cannot get the UPC_Generic_ExpressionSet to work properly. The code runs, but a boxplot() function of the exprs() shows data that is not normalized. ...
written 4.5 years ago by PyPer20
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Normalizing Expressionset Exprs without Raw CEL files
... I know typically you download CEL files then run them through something like readaffy and then use RMA normalization. However, many datasets on GEO do not have the associated raw CEL files. Furthermore downloading multiple CEL files is both long and tedious. For some of the things i'm doing, norma ...
normalization geoquery written 4.5 years ago by PyPer20 • updated 4.5 years ago by Stephen Piccolo560
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Compare Row.names and ID from GSE datasets
... I am annotating data from a GSE dataset. I want to check that the row.names are equivalent to ID to ensure that there are no mistakes. gse10072 <- getGEO('gse10072', GSEMATRIX=TRUE) g72 <- gse10072[[1]] total <- pData(featureData(g72)) t1 <- data.frame(row.names(total)) t2 <- data.f ...
geoquery gse identical row.names written 4.5 years ago by PyPer20 • updated 4.5 years ago by Sean Davis21k
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Comment: C: Annotation from Submitter GPL in GSE dataset
... Thanks for the answer! very helpful. Just a couple of follow up questions From the code you've provided, you've matched the GB_LIST to the known gene names. I'm still a bit confused about the GB_LIST. If these are known Genebank accession numbers, shouldn't they easily match? In other words, why do ...
written 4.5 years ago by PyPer20
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Annotation from Submitter GPL in GSE dataset
... I've recently started trying to process data from the GEO datasets that are publically available. Unfortunately my R skills are still quite not up to par. I've been working with a specific set in particular GSE3933 the code is simply to extract the expression for each sample then match it with the ...
annotation geoquery written 4.5 years ago by PyPer20 • updated 4.5 years ago by James W. MacDonald49k

Latest awards to PyPer

Popular Question 4.4 years ago, created a question with more than 1,000 views. For Normalizing Expressionset Exprs without Raw CEL files
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Annotation from Submitter GPL in GSE dataset

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