How to merge to two cel objects imported by oligo package
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@dai-hongying-4801
Last seen 7.2 years ago
Hi, Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now. Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works. R>biocLite("pd.moex.1.0.st.v1") R>biocLite("olig") R>exonCELs <- list.celfiles(full.names = TRUE) R>affyExonFS1 <- read.celfiles(exonCELs[1:6]) #First read 6 CEL files, then save the results and clear the memory R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work R>library(affy) R> merge.AffyBatch(affyExonFS1,affyExonFS2) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "intensity", for signature "ExonFeatureSet" Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package. Thanks! Daisy ________________________________ Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer@cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. [[alternative HTML version deleted]]
affy oligo affy oligo • 1.4k views
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@benilton-carvalho-1375
Last seen 20 months ago
Brazil/Campinas/UNICAMP
FS3 <- combine(affyExonFS1, affyExonFS2) cheers, b On 11 August 2011 18:36, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: > Hi, > > Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now. > Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works. > > R>biocLite("pd.moex.1.0.st.v1") > R>biocLite("olig") > R>exonCELs <- list.celfiles(full.names = TRUE) > > R>affyExonFS1 <- read.celfiles(exonCELs[1:6]) ?#First read 6 CEL files, then save the results and clear the memory > R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files > > Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work > R>library(affy) > R> merge.AffyBatch(affyExonFS1,affyExonFS2) > > Error in function (classes, fdef, mtable) ?: > unable to find an inherited method for function "intensity", for signature "ExonFeatureSet" > > Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package. > > Thanks! > > Daisy > > > ________________________________ > Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)
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Dr. Carvalho, thank you very much! I tried to combine CEL files but I don't have enough RAM(2.75GB). R> FS3 <- combine(affyExonFS1, affyExonFS2) Error: cannot allocate vector of size 300.0 Mb Then I tried to combine RMA processed data instead of combining CEL files. R> exonCELs<-list.celfiles(full.names = TRUE) R> affyExonFS1<-read.celfiles(exonCELs[1:6]) #Read 6 CEL files R> exonCore1 <- rma(affyExonFS1, target = "core") R> affyExonFS2 <- read.celfiles(exonCELs[7:12]) #Read 6 CEL files R> exonCore2 <- rma(affyExonFS2, target = "core") R> exonCore<-combine(exonCore1,exonCore2) Warning messages: 1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 6 string mismatches 2: data frame column 'exprs' levels not all.equal My question: (A) Is it okay to ignore the warning message and use the combined rma data, exonCore, for further analysis? (B) Is there any way to improve "exonCore<-combine(exonCore1,exonCore2)" code? R > dim(exonCore1) Features Samples 23332 6 R > dim(exonCore2) Features Samples 23332 6 Daisy -----Original Message----- From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Thursday, August 11, 2011 6:57 PM To: Dai, Hongying, Cc: bioconductor at r-project.org Subject: Re: [BioC] How to merge to two cel objects imported by oligo package FS3 <- combine(affyExonFS1, affyExonFS2) cheers, b On 11 August 2011 18:36, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: > Hi, > > Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now. > Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works. > > R>biocLite("pd.moex.1.0.st.v1") > R>biocLite("olig") > R>exonCELs <- list.celfiles(full.names = TRUE) > > R>affyExonFS1 <- read.celfiles(exonCELs[1:6]) ?#First read 6 CEL files, then save the results and clear the memory > R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files > > Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work > R>library(affy) > R> merge.AffyBatch(affyExonFS1,affyExonFS2) > > Error in function (classes, fdef, mtable) ?: > unable to find an inherited method for function "intensity", for signature "ExonFeatureSet" > > Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package. > > Thanks! > > Daisy > > > ________________________________ > Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)
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Hi Daisy, consider using the following: library(ff) library(oligo) x = read.celfiles(list.celfiles()) exonCore = rma(x, target='core') This will allow you to read in and preprocess all data at once... It will be slower, but you will gain from the fact that you're using all of your samples at once. About the warning, I need to investigate what is going on. It appears that you can safely disregard it (but double check the contents of protocolData(exonCore) ). b On 12 August 2011 03:10, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: > Dr. Carvalho, thank you very much! > > I tried to combine CEL files but I don't have enough RAM(2.75GB). > > R> FS3 <- combine(affyExonFS1, affyExonFS2) > Error: cannot allocate vector of size 300.0 Mb > > Then I tried to combine RMA processed data instead of combining CEL files. > > R> exonCELs<-list.celfiles(full.names = TRUE) > R> affyExonFS1<-read.celfiles(exonCELs[1:6]) #Read 6 CEL files > R> exonCore1 <- rma(affyExonFS1, target = "core") > R> affyExonFS2 <- read.celfiles(exonCELs[7:12]) #Read 6 CEL files > R> exonCore2 <- rma(affyExonFS2, target = "core") > > R> exonCore<-combine(exonCore1,exonCore2) > Warning messages: > 1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 6 string mismatches > 2: data frame column 'exprs' levels not all.equal > > My question: > (A) Is it okay to ignore the warning message and use the combined rma data, exonCore, for further analysis? > > (B) Is there any way to improve "exonCore<-combine(exonCore1,exonCore2)" code? > > R > dim(exonCore1) > Features ?Samples > ? 23332 ? ? ? ?6 > R > dim(exonCore2) > Features ?Samples > ? 23332 ? ? ? ?6 > > Daisy > > > > > > > -----Original Message----- > From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] > Sent: Thursday, August 11, 2011 6:57 PM > To: Dai, Hongying, > Cc: bioconductor at r-project.org > Subject: Re: [BioC] How to merge to two cel objects imported by oligo package > > FS3 <- combine(affyExonFS1, affyExonFS2) > > cheers, > b > > On 11 August 2011 18:36, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: >> Hi, >> >> Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now. >> Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works. >> >> R>biocLite("pd.moex.1.0.st.v1") >> R>biocLite("olig") >> R>exonCELs <- list.celfiles(full.names = TRUE) >> >> R>affyExonFS1 <- read.celfiles(exonCELs[1:6]) ?#First read 6 CEL files, then save the results and clear the memory >> R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files >> >> Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work >> R>library(affy) >> R> merge.AffyBatch(affyExonFS1,affyExonFS2) >> >> Error in function (classes, fdef, mtable) ?: >> unable to find an inherited method for function "intensity", for signature "ExonFeatureSet" >> >> Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package. >> >> Thanks! >> >> Daisy >> >> >> ________________________________ >> Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Successful people ask better questions, and as a result, they get > better answers. (Tony Robbins) > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)
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Dr. Carvalho, I followed your code and IT WORKS!!! Thank you so much! I struggled an entire week trying to get this done. I have tried library(ff) before per Cary Vincent's suggestion. Since I might have other computer issues, library(ff) did not work at the beginning. When I sorted out other computer issues and restarted R, I did not invoke library(ff) as I thought it had been included in library(oligo). Again, I really appreciate your help! Best, Daisy -----Original Message----- From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com] Sent: Friday, August 12, 2011 1:54 AM To: Dai, Hongying, Cc: bioconductor at r-project.org Subject: Re: [BioC] How to merge to two cel objects imported by oligo package Hi Daisy, consider using the following: library(ff) library(oligo) x = read.celfiles(list.celfiles()) exonCore = rma(x, target='core') This will allow you to read in and preprocess all data at once... It will be slower, but you will gain from the fact that you're using all of your samples at once. About the warning, I need to investigate what is going on. It appears that you can safely disregard it (but double check the contents of protocolData(exonCore) ). b On 12 August 2011 03:10, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: > Dr. Carvalho, thank you very much! > > I tried to combine CEL files but I don't have enough RAM(2.75GB). > > R> FS3 <- combine(affyExonFS1, affyExonFS2) > Error: cannot allocate vector of size 300.0 Mb > > Then I tried to combine RMA processed data instead of combining CEL files. > > R> exonCELs<-list.celfiles(full.names = TRUE) > R> affyExonFS1<-read.celfiles(exonCELs[1:6]) #Read 6 CEL files > R> exonCore1 <- rma(affyExonFS1, target = "core") > R> affyExonFS2 <- read.celfiles(exonCELs[7:12]) #Read 6 CEL files > R> exonCore2 <- rma(affyExonFS2, target = "core") > > R> exonCore<-combine(exonCore1,exonCore2) > Warning messages: > 1: In alleq(levels(x[[nm]]), levels(y[[nm]])) : 6 string mismatches > 2: data frame column 'exprs' levels not all.equal > > My question: > (A) Is it okay to ignore the warning message and use the combined rma data, exonCore, for further analysis? > > (B) Is there any way to improve "exonCore<-combine(exonCore1,exonCore2)" code? > > R > dim(exonCore1) > Features ?Samples > ? 23332 ? ? ? ?6 > R > dim(exonCore2) > Features ?Samples > ? 23332 ? ? ? ?6 > > Daisy > > > > > > > -----Original Message----- > From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] > Sent: Thursday, August 11, 2011 6:57 PM > To: Dai, Hongying, > Cc: bioconductor at r-project.org > Subject: Re: [BioC] How to merge to two cel objects imported by oligo package > > FS3 <- combine(affyExonFS1, affyExonFS2) > > cheers, > b > > On 11 August 2011 18:36, Dai, Hongying, <hdai at="" cmh.edu=""> wrote: >> Hi, >> >> Thank Cary Vincent and Christian for answering my previous question. I'm able to import Mouse Exon 1.0 ST array now. >> Due to my RAM memory restriction, I can only import one CEL file each time. Here is my code and it works. >> >> R>biocLite("pd.moex.1.0.st.v1") >> R>biocLite("olig") >> R>exonCELs <- list.celfiles(full.names = TRUE) >> >> R>affyExonFS1 <- read.celfiles(exonCELs[1:6]) ?#First read 6 CEL files, then save the results and clear the memory >> R>affyExonFS2 <- read.celfiles(exonCELs[6:12]) # Read another 6 CEL files, and load the first 6 CEL files >> >> Now my question is how to merge affyExonFS1 and affyExonFS2. My following code did not work >> R>library(affy) >> R> merge.AffyBatch(affyExonFS1,affyExonFS2) >> >> Error in function (classes, fdef, mtable) ?: >> unable to find an inherited method for function "intensity", for signature "ExonFeatureSet" >> >> Can anyone help me to merge CEL batches, affyExonFS1 and affyExonFS2, imported by oligo package read.celfiles() function? Note CEL is imported by oligo package instead of affy package. I could not find a merge batch function in the oligo package. >> >> Thanks! >> >> Daisy >> >> >> ________________________________ >> Electronic mail from Children's Mercy Hospitals and Clinics. This communication is intended only for the use of the addressee. It may contain information that is privileged or confidential under applicable law. If you are not the intended recipient or the agent of the recipient, you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited. If you have received this communication in error, please immediately forward the message to Children's Mercy Hospital's Information Security Officer via return electronic mail at informationsecurityofficer at cmh.edu and expunge this communication without making any copies. Thank you for your cooperation. >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > Successful people ask better questions, and as a result, they get > better answers. (Tony Robbins) > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)
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