User: Peevi Ijkl

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Peevi Ijkl170
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Posts by Peevi Ijkl

<prev • 17 results • page 2 of 2 • next >
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Comment: C: class label
... Hello martin i know that multtest works..but for it to work correctly i need to create a class label right..which am not able to ..i am attching the original txt file that i created..it is tab delimited.. ID disease GSM469509.CEL A GSM469510.CEL A GSM469511.CEL A GSM469512.CEL A GSM46 ...
written 8.8 years ago by Peevi Ijkl170
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class label
... Hello ok my phenodata(target.txt) looks something like this 1.CEL A 1.CEL A 3.CEL A 4.CEL H 5.CEL H 6.CEL H i loaded the above into my R using library(affy) library(simpleaffy) eset<-read.AnnotatedDataFrame("target.txt", header=T, row.names=1, sep="\t" ) to view my data: pData(eset) th ...
normalization multtest written 8.8 years ago by Peevi Ijkl170 • updated 8.8 years ago by Martin Morgan ♦♦ 23k
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test class label
... Hi I wanted to know if there is an alternative code for creating class labels for multtest? I used cl <- as.numeric(pd$Diabetic == "y" ) ...my phenodata has diabetic and non diabetic data ...but this code isnt working..could some help please thanks peevi [[alternative HTML version de ...
written 8.8 years ago by Peevi Ijkl170 • updated 8.8 years ago by Martin Morgan ♦♦ 23k
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codes
... Hi Does anyone have codes for the following: 1) Read CEL files 2) normalization 3) dChip 4) multtest 5 finding Significant genes 6) hierarchical clustering 7) box plots 8)histograms and anything else that can be useful pevi [[alternative HTML version deleted]] ...
written 8.8 years ago by Peevi Ijkl170 • updated 8.8 years ago by Steve Lianoglou12k
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permutation
... Hi I am trying to do a permutation with a p cut off of 0.05 from a dataset and generate pathways.can someone tell me how to do it thanks peevi [[alternative HTML version deleted]] ...
pathways written 8.9 years ago by Peevi Ijkl170 • updated 8.9 years ago by Steve Lianoglou12k
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nsFilter
... Hello List I wanted to perform nonspecific filtering on my expression set. i gave the following code >f1<-function(x) IQR > 0.5) >ff<-filterfun(f1) >selected<-genefilter(data2,ff) >sum(selected) i knw this is for genefilter..but can the above be used for non specific filteri ...
genefilter written 8.9 years ago by Peevi Ijkl170 • updated 8.9 years ago by Vincent J. Carey, Jr.6.3k
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gene expression set using KEGG
... Hi List I performed qc on some data and then i did gcrma on the the raw data and converted into an expression set object(data.m).i then performed filtering using rowSds(data.f). Now I am trying to perform GeneSetCollection for KEGG but getting the following error. >gsc<-GeneSetCollection(data ...
gcrma written 8.9 years ago by Peevi Ijkl170 • updated 8.9 years ago by Martin Morgan ♦♦ 23k

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