User: pingzhao Hu

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pingzhao Hu210
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11 years, 7 months ago
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15 years, 9 months ago
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p**@sickkids.ca

Posts by pingzhao Hu

<prev • 21 results • page 2 of 3 • next >
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GeneChip Mouse Gene 1.0 ST annotation
... Hi Marco, Are these not what you want? from here: [1]http://www.affymetrix.com/support/technical/byproduct.affx?produ ct=mogene -1_0-st-v1 [] [2] MoGene-1_0-st-v1 Annotations CSV README (26 KB, 9/5/07) [] [3] MoGene-1_0-st-v1 Transcript Cluster Annotations, CSV (11 MB, 9/1 ...
written 12.1 years ago by pingzhao Hu210
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how to read in affy snp 500K arrays
... Hi Allen, You can also try PLASQ package http://genome.dfci.harvard.edu/~tlaframb/PLASQ/, which do normalization and CNV inference using affy 500k data. pingzhao ======================================== Pingzhao Hu Statistical Analysis Facility The Centre for Applied Genomics (TCAG) The Hospital ...
affy written 12.1 years ago by pingzhao Hu210
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Exploding PLASQ Inevitable : slot exprs AffyBatch
... Hi Richard, You need to change a little bit the code. round(ReadAffy(filenames = paste(celFolder, i, sep = "/"))@exprs) to round(exprs(ReadAffy(filenames = paste(celFolder,i, sep = "/"))))) in celExtNorm and celExtract functions. Thanks for Ben told me this before. Pingzhao ...
written 12.4 years ago by pingzhao Hu210
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Answer: A: Is it possible to fit a hierarchical linear model in LIMMA?
... Hi, Say two groups A and B. Each group has 10 individuals. Assume that we have two variables: Y and X. Therefore, the hierarchical linear model will like: Yij=B0i+B1Xij+ERRORij, (i=A,B; j=1,2,...,10) We are interested in testing the significance of B1. Although some R packages can do this job, we ...
written 13.8 years ago by pingzhao Hu210
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Is it possible to fit a hierarchical linear model in LIMMA?
... Hi, Say two groups A and B. Each group has 10 individuals. Assume that we have two variables: Y and X. Therefore, the hierarchical linear model will like: Yij=B0i+B1Xij+ERRORij, (i=A,B; j=1,2,...,10) We are interested in testing the significance of B1. Although some R packages can do this job, we ...
limma written 13.8 years ago by pingzhao Hu210
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Chromosome location for probes
... Hi, For a probeset, say 1010_at, its chromosome location (chr22) is 49004598-49011189. Assume the probeset has 16 PM probes, how can I get these probes' chromosome locations? Can any functions in bioconductor packages do this job ? Thanks, Pingzhao ...
written 13.9 years ago by pingzhao Hu210 • updated 13.9 years ago by Oosting, J. PATH550
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problem to read .CEL file
... Hi all, I have a affy dataset ( hgu95av2cdf ) which has 207 arrays. One of these .CEL files can not be read from our supercomputer. The error message is as follows: > myaffybatch<-ReadAffy(verbose=TRUE) 1 reading /export/scratch4/pinghu/CL2001031608AA.CEL ...done. instanciating an AffyBatch ...
cdf affy written 15.3 years ago by pingzhao Hu210
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design matrix and lmFit problems in limma
... Hi, I have an Affymetrix dataset. There are 24 arrays. There are three factors: time, sex (M and F) and strain (NOD,R and D4). Sex has two levels and strain has 3 levels. I am only interested in interaction between sex and strain. So the formula will like: ~time+sex*strain. The question I want t ...
affy written 15.6 years ago by pingzhao Hu210
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RMA
... I simulated PM and MM matrix (named pm.raw and mm.raw) (say 100 * 16 *15 --100 genes, 16 probes and 15 chips) Now I try to estimate expression values using RMA. Essentially, RMA has 3 steps: 1) background correction: pm.bgc<- apply(pm.raw, 2, bg.adjust) this is not working. ------------------ ...
probe written 15.7 years ago by pingzhao Hu210
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update topTable question in limma
... Hi, I am using limma. Here is a error I met SubM is a 19k by 6 matrix > design [1] 1 1 1 -1 -1 -1 > PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation=mycor$cor,weig hts=NULL) > PMAfit<-ebayes(PMAfit) > topT<-topTable(PMAfit,number=200,sort.by="P",genelist=genelis ...
limma written 15.7 years ago by pingzhao Hu210

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Popular Question 11.6 years ago, created a question with more than 1,000 views. For design matrix and lmFit problems in limma

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