User: rohan bareja

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rohan bareja200
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Posts by rohan bareja

<prev • 21 results • page 1 of 3 • next >
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DEseq package statistical test
... Hi all,   I use DESeq2 package for differential expression analysis ,where df is the the count data.     data1<-as.matrix(df) ##do differential expression library(DESeq2) dds <- DESeqDataSetFromMatrix(countData = data1,colData = pdata,design = ~ condition ) #reference is group2,so up me ...
deseq2 differential gene expression written 12 weeks ago by rohan bareja200 • updated 12 weeks ago by Steve Lianoglou12k
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Comment: C: Case vs Control Information,Diseases
... Thanks Sean for your quick response! The other part I am stuck on is the gene information.I discussed this with you earlier so I have the code which should run but not getting the expected results. The issue comes when I am looping over my gplllist object and when there are more than 10 gpls,and ...
written 4.0 years ago by rohan bareja200
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Case vs Control Information,Diseases
... Hi, I would like to get information on which samples are cases and which are controls. I am using the following commands : #creating GDS list annotgds = dbGetQuery(con,"select GDS from gds") #getting data for first 20 GDS gdslist <- sapply(annotgds[1:20,1],getGEO) #using column method get the ...
written 4.0 years ago by rohan bareja200 • updated 4.0 years ago by Sean Davis21k
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Fw: Meta data for gene from GEO
... On Thursday, 28 November 2013 2:12 PM, rohan bareja wrote: Hi Sean, Thanks for your help!I am trying to get the gene ids for first 3 gpl list objects here, using this: i). genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene ID']})) This is the result of first 3 gene id ...
annotation gpls geoquery geometadb written 4.0 years ago by rohan bareja200
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Meta data for gene from GEO
... Hi Sean, I am trying to get the gene ids for genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene ID']})) On Monday, 25 November 2013 2:33 PM, Sean Davis wrote: On Mon, Nov 25, 2013 at 2:22 PM, rohan bareja wrote: Hi Sean, > >the answer was really helpful.I am ...
annotation gpls geoquery geometadb written 4.0 years ago by rohan bareja200 • updated 4.0 years ago by Sean Davis21k
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Comment: C: Meta data for gene from GEO
... Hi Sean, Thanks for your help!I am trying to get the gene ids for first 3 gpl list objects here, using this: i). genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene ID']})) This is the result of first 3 gene id's in first gpl object(GPL13) using the command above. "1""GPL13" ...
written 4.0 years ago by rohan bareja200
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Comment: C: Meta data for gene from GEO
... Hi Sean, the answer was really helpful.I am using this to get all the annotations for gpl in this object ,since there are 438 gpl's in annotgpl object. gpllist <- sapply(annotgpl[1:438,1],getGEO,AnnotGPL=TRUE) But this is a list object, and I am unable to access this using a Table function. b ...
written 4.0 years ago by rohan bareja200
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Answer: A: Normalization in Coverage
... Hi Valerie, Thats what I wanted to do but I dont know how to write a normalization function for Coverage.. Would it be somewhat calculating RPKMs ??If yes how should I do that? Thanks, Rohan [[alternative HTML version deleted]] ...
written 6.0 years ago by rohan bareja200
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Normalization in Coverage
... Hi everyone, I am looking at coverage in certain continuous intervals of a gene.I have got this Views object. However Could I do normalization of the reads  in this object which is very necessary in doing any analysis further? ir <- IRanges(c(90645249,90645349,90645449,90645549,90645649,906 ...
coverage normalization written 6.1 years ago by rohan bareja200
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Normalization in Coverage
... Hi everyone, I am looking at coverage in certain intervals of a chromosome.I have got this Views object.However Could I do normalization of the reads which is very necessary in doing any analysis further? ir <- IRanges(c(90645249,90645349,90645449,90645549,90645649,90645749, 90645849,90645949,90 ...
coverage normalization written 6.1 years ago by rohan bareja200

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