Question: Combining GEOquery with samr or siggenes
0
gravatar for Voke AO
8.3 years ago by
Voke AO760
Voke AO760 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? Thanks a bunch. ~V
siggenes geoquery • 688 views
ADD COMMENTlink modified 8.3 years ago • written 8.3 years ago by Voke AO760
Answer: Combining GEOquery with samr or siggenes
0
gravatar for Sean Davis
8.3 years ago by
Sean Davis21k
United States
Sean Davis21k 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"
ADD COMMENTlink written 8.3 years ago by Sean Davis21k
Answer: Combining GEOquery with samr or siggenes
0
gravatar for Sean Davis
8.3 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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" >> >
ADD COMMENTlink written 8.3 years ago by Sean Davis21k
Answer: Combining GEOquery with samr or siggenes
0
gravatar for Voke AO
8.3 years ago by
Voke AO760
Voke AO760 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? Thanks a bunch. ~V
ADD COMMENTlink written 8.3 years ago by Voke AO760
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