Question: GEOquery and different GPL: handle of GSE
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gravatar for claudio.is@libero.it
12.8 years ago by
claudio.is@libero.it210 wrote:
Dear BioC, I'm downloading a dataset from NCBI GEO with GEOquery, in particular GSE3654, which is composed by different GPL platforms; according to the vignette I have to split the dataset according to the GPLs, but I found I was not able to handle the GSE classes and sub-index it. Can you help me? -- Claudio ------------------------------------------------------ Dimagrire in 30 Giorni, Soddisfatti o Rimborsati! Clicca qui http://click.libero.it/webnation7feb2007
gpls geoquery • 689 views
ADD COMMENTlink modified 12.8 years ago • written 12.8 years ago by claudio.is@libero.it210
Answer: GEOquery and different GPL: handle of GSE
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gravatar for Sean Davis
12.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
claudio.is at libero.it wrote: > Dear BioC, > > I'm downloading a dataset from NCBI GEO with GEOquery, in particular GSE3654, which is composed by different GPL platforms; according to the vignette I have to split the dataset according to the GPLs, but I found I was not able to handle the GSE classes and sub-index it. Can you help me? > Claudio, I'm glad to hear you have gotten the data downloaded and into a GSE object. In what column of the GSM tables are you interested? Also, what have you tried? I can comment more fully with that information. Sean
ADD COMMENTlink written 12.8 years ago by Sean Davis21k
Answer: GEOquery and different GPL: handle of GSE
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gravatar for claudio.is@libero.it
12.8 years ago by
claudio.is@libero.it210 wrote:
---------- Initial Header ----------- >From : "Sean Davis" sdavis2 at mail.nih.gov To : "claudio.is at libero.it" claudio.is at libero.it Cc : "bioconductor" bioconductor at stat.math.ethz.ch Date : Wed, 07 Feb 2007 21:28:21 -0500 Subject : Re: [BioC] GEOquery and different GPL: handle of GSE I will show you the script for another GSE accession I have it right now, library(GEOquery) library(Biobase) #downloading and storing in GSE gse2564=getGEO("GSE2564") #Check for GPL of each platform gsmplatforms <- lapply(GSMList(gse2564), function(x) { Meta(x)$platform }) ## now I wanted to sub-index the gse according to the field $platoform, and as when I run GSMList(gse2564)[1] the object is a GSM, I suppose that the following line should works GSMList(gse2564)[1]$platform but I retrive a null results. > claudio.is at libero.it wrote: > > Dear BioC, > > > > I'm downloading a dataset from NCBI GEO with GEOquery, in particular GSE3654, which is composed by different GPL platforms; according to the vignette I have to split the dataset according to the GPLs, but I found I was not able to handle the GSE classes and sub- index it. Can you help me? > > > Claudio, > > I'm glad to hear you have gotten the data downloaded and into a GSE > object. In what column of the GSM tables are you interested? Also, > what have you tried? I can comment more fully with that information. > > Sean > ------------------------------------------------------ Passa a Infostrada. ADSL e Telefono senza limiti e senza canone Telecom http://click.libero.it/infostrada8feb07
ADD COMMENTlink written 12.8 years ago by claudio.is@libero.it210
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