Hi, Is it possible to somehow have a code that can pull out several GDS info (like a batch process) using GEOquery in a way that they can subsequently be analyzed with SAM or Siggenes in a kind of loop? Thanks a bunch. ~V

On Thu, Sep 1, 2011 at 5:57 AM, Voke AO <ovokeraye at="" gmail.com=""> wrote: > Hi, > > Is it possible to somehow have a code that can pull out several GDS > info (like a batch process) using GEOquery in a way that they can > subsequently be analyzed with SAM or Siggenes in a kind of loop? Yes. Here is a simple example. You will need to supply the code to do any actual analysis and return the actual result, but I hope you get the idea. I used sapply as the loop structure, but you could use any loop structure that you like. Hope that helps. Sean > gdslist = c('GDS3717','GDS3718','GDS3719') > analysisfunc = function(gdsid) { gdsdat = getGEO(gdsid,destdir=".") gdseset = GDS2eSet(gdsdat) message("DO SIGGENES STUFF HERE") return(sprintf("Results from %s would be here",gdsid)) } > resultlist = sapply(gdslist,analysisfunc) File stored at: ./GDS3717.soft.gz File stored at: /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL570.annot.gz DO SIGGENES STUFF HERE File stored at: ./GDS3718.soft.gz File stored at: /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL1261.annot.gz DO SIGGENES STUFF HERE File stored at: ./GDS3719.soft.gz File stored at: /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL1319.annot.gz DO SIGGENES STUFF HERE There were 50 or more warnings (use warnings() to see the first 50) > resultlist GDS3717 GDS3718 "Results from GDS3717 would be here" "Results from GDS3718 would be here" GDS3719 "Results from GDS3719 would be here"

On Thu, Sep 1, 2011 at 7:40 AM, Voke AO <ovokeraye at="" gmail.com=""> wrote: > Hi, > > This would work if I had the exact sample sizes and knew what columns > are cases or controls. I guess my question is more like...if I knew > 100 GDS files had data related to a disease of interest, it would be a > vicious process to go through each one and create a cl or cls file to > correspond to the data. In such a situation, will it be possible to > have a code that will > 1. Go through the specified number of GDS files > 2. Detect the different classes of samples and assign numbers > accordingly for SAM/Siggenes for each GDS file, that will eventually > be called back in the loop process for the SAM/Siggenes analysis of > each file. > > I'm very much a beginner in programming so, I'm hoping I don't sound too naive. Unfortunately, there will be some programming involved here. As for the class info, the phenoData slot of an ExpressionSet resulting from a call to GDS2eSet will be fully populated. Often, there will be a standard column "disease.state" that you could use to create the cls object. > gds = getGEO("GDS10") > eset = GDS2eSet(gds) > pData(eset)$disease.state [1] diabetic diabetic diabetic-resistant diabetic-resistant [5] diabetic-resistant diabetic-resistant diabetic-resistant diabetic-resistant [9] diabetic-resistant diabetic-resistant nondiabetic nondiabetic [13] nondiabetic nondiabetic diabetic diabetic [17] diabetic-resistant diabetic-resistant diabetic-resistant diabetic-resistant [21] diabetic-resistant diabetic-resistant diabetic-resistant diabetic-resistant [25] nondiabetic nondiabetic nondiabetic nondiabetic Levels: diabetic diabetic-resistant nondiabetic Hope that helps. Sean > Thanks again. > > ~V > > On Thu, Sep 1, 2011 at 12:50 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Thu, Sep 1, 2011 at 5:57 AM, Voke AO <ovokeraye at="" gmail.com=""> wrote: >>> Hi, >>> >>> Is it possible to somehow have a code that can pull out several GDS >>> info (like a batch process) using GEOquery in a way that they can >>> subsequently be analyzed with SAM or Siggenes in a kind of loop? >> >> Yes. ?Here is a simple example. ?You will need to supply the code to >> do any actual analysis and return the actual result, but I hope you >> get the idea. ?I used sapply as the loop structure, but you could use >> any loop structure that you like. >> >> Hope that helps. >> >> Sean >> >>> gdslist = c('GDS3717','GDS3718','GDS3719') >>> analysisfunc = function(gdsid) { >> ?gdsdat = getGEO(gdsid,destdir=".") >> ?gdseset = GDS2eSet(gdsdat) >> ?message("DO SIGGENES STUFF HERE") >> ?return(sprintf("Results from %s would be here",gdsid)) >> } >>> resultlist = sapply(gdslist,analysisfunc) >> File stored at: >> ./GDS3717.soft.gz >> File stored at: >> /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL570.annot.gz >> DO SIGGENES STUFF HERE >> File stored at: >> ./GDS3718.soft.gz >> File stored at: >> /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL1261.annot.gz >> DO SIGGENES STUFF HERE >> File stored at: >> ./GDS3719.soft.gz >> File stored at: >> /var/folders/23/234W5ZnqHPih- U4YppHVCU+++TI/-Tmp-//RtmpgeksBL/GPL1319.annot.gz >> DO SIGGENES STUFF HERE >> There were 50 or more warnings (use warnings() to see the first 50) >>> resultlist >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? GDS3717 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?GDS3718 >> "Results from GDS3717 would be here" "Results from GDS3718 would be here" >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? GDS3719 >> "Results from GDS3719 would be here" >> >

Hi, Is it possible to somehow have a code that can pull out several GDS info (like a batch process) using GEOquery in a way that they can subsequently be analyzed with SAM or Siggenes in a kind of loop? Thanks a bunch. ~V