Question: CGHcall and Normalization
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gravatar for Salih Tuna
8.2 years ago by
Salih Tuna30
Salih Tuna30 wrote:
Hi, i am trying to use the normalization function from CGHcall library. The command i use is normal.fullData <- normalize(fullData, method = "median", cellularity = 1) and i get the following error message. How can i solve this issue. Error in function (classes, fdef, mtable) : unable to find an inherited method for function "copynumber", for signature "data.frame" best, salih -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. [[alternative HTML version deleted]]
normalization cghcall • 818 views
ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Salih Tuna30
Answer: CGHcall and Normalization
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gravatar for Martin Morgan
8.2 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
On 06/08/2011 08:47 AM, Salih Tuna wrote: > Hi, > > i am trying to use the normalization function from CGHcall library. > > The command i use is > > > > normal.fullData<- normalize(fullData, method = "median", cellularity = > 1) > > and i get the following error message. How can i solve this issue. > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "copynumber", for > signature "data.frame" Hi Salih -- If I example(CGHcall) and look at how normalize() is used, the first argument is 'raw.data' and it is > class(raw.data) [1] "cghRaw" attr(,"package") [1] "CGHbase" if instead I > normalize(data.frame()) Applying median normalization ... Error in function (classes, fdef, mtable) : unable to find an inherited method for function "copynumber", for signature "data.frame" so perhaps you are trying to use a data.frame instead of an object of 'cghRaw', i.e., your earlier work flow needs to be adjusted. If you need more help, it is best to post a reproducible example, starting from sample data available in the package. Hope that helps, Martin > > best, > > salih > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 8.2 years ago by Martin Morgan ♦♦ 23k
Answer: CGHcall and Normalization
0
gravatar for Salih Tuna
8.2 years ago by
Salih Tuna30
Salih Tuna30 wrote:
Hi Martin, Thanks for your reply. I managed to run the code. AS you said I needed to adjust the data. But now the output seems something like this: normalized.data cghRaw (storageMode: lockedEnvironment) assayData: 3552 features, 5 samples element names: copynumber phenoData sampleNames: AdCA10, SCC27, ..., SCC39 (5 total) varLabels and varMetadata description: none featureData featureNames: RP11-465B22, RP4-785P20, ..., CTB-99K24 (3552 total) fvarLabels and fvarMetadata description: Chromosome: Chromosomal position Start: Basepair position start End: Basepair position end experimentData: use 'experimentData(object)' Annotation: This might be a very stupid question but I was expecting to see the normalized data which is the same dimension as the raw data. I am sure I can access the normalized data which is the same dimension as the raw data. But I don't know how. Could you please show me how to do this? Best, salih -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: 11 June 2011 16:24 To: Salih Tuna Cc: bioconductor at r-project.org Subject: Re: [BioC] CGHcall and Normalization On 06/08/2011 08:47 AM, Salih Tuna wrote: > Hi, > > i am trying to use the normalization function from CGHcall library. > > The command i use is > > > > normal.fullData<- normalize(fullData, method = "median", cellularity = > 1) > > and i get the following error message. How can i solve this issue. > > Error in function (classes, fdef, mtable) : > > unable to find an inherited method for function "copynumber", for > signature "data.frame" Hi Salih -- If I example(CGHcall) and look at how normalize() is used, the first argument is 'raw.data' and it is > class(raw.data) [1] "cghRaw" attr(,"package") [1] "CGHbase" if instead I > normalize(data.frame()) Applying median normalization ... Error in function (classes, fdef, mtable) : unable to find an inherited method for function "copynumber", for signature "data.frame" so perhaps you are trying to use a data.frame instead of an object of 'cghRaw', i.e., your earlier work flow needs to be adjusted. If you need more help, it is best to post a reproducible example, starting from sample data available in the package. Hope that helps, Martin > > best, > > salih > > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD COMMENTlink written 8.2 years ago by Salih Tuna30
On 06/13/2011 08:01 AM, Salih Tuna wrote: > Hi Martin, > Thanks for your reply. I managed to run the code. AS you said I needed > to adjust the data. > But now the output seems something like this: > > normalized.data > cghRaw (storageMode: lockedEnvironment) > assayData: 3552 features, 5 samples > element names: copynumber > phenoData > sampleNames: AdCA10, SCC27, ..., SCC39 (5 total) > varLabels and varMetadata description: none > featureData > featureNames: RP11-465B22, RP4-785P20, ..., CTB-99K24 (3552 total) > fvarLabels and fvarMetadata description: > Chromosome: Chromosomal position > Start: Basepair position start > End: Basepair position end > experimentData: use 'experimentData(object)' > Annotation: > > This might be a very stupid question but I was expecting to see the > normalized data which is the same dimension as the raw data. I am sure I > can access the normalized data which is the same dimension as the raw > data. But I don't know how. Could you please show me how to do this? The docs for ?normalize say that the 'value' returned is a data.frame, but... class(normalized.data) tells me this is a cghRaw object (as does the display, above). So I looked at ?cghRaw and found that I could extract the copy number data with copynumber(normalized.data) And it seems to be different from (i.e., normalized) the raw data > example(CGHcall) [snip] > colSums(copynumber(raw.data)) AdCA10 SCC27 SCC32 SCC36 SCC39 -215.51938 46.58693 -153.71559 398.60994 518.95828 > colSums(copynumber(normalized.data)) AdCA10 SCC27 SCC32 SCC36 SCC39 -127.75115 -39.93650 -69.26762 134.13213 409.15257 so the documentation (also browseVignettes(package="CGHcall")) seems to be your friend (if a little difficult to navigate). Martin > > Best, > salih > > -----Original Message----- > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] > Sent: 11 June 2011 16:24 > To: Salih Tuna > Cc: bioconductor at r-project.org > Subject: Re: [BioC] CGHcall and Normalization > > On 06/08/2011 08:47 AM, Salih Tuna wrote: >> Hi, >> >> i am trying to use the normalization function from CGHcall library. >> >> The command i use is >> >> >> >> normal.fullData<- normalize(fullData, method = "median", cellularity = >> 1) >> >> and i get the following error message. How can i solve this issue. >> >> Error in function (classes, fdef, mtable) : >> >> unable to find an inherited method for function "copynumber", for >> signature "data.frame" > > Hi Salih -- > > If I > > example(CGHcall) > > and look at how normalize() is used, the first argument is 'raw.data' > and it is > > > class(raw.data) > [1] "cghRaw" > attr(,"package") > [1] "CGHbase" > > if instead I > > > normalize(data.frame()) > Applying median normalization ... > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "copynumber", for > signature "data.frame" > > so perhaps you are trying to use a data.frame instead of an object of > 'cghRaw', i.e., your earlier work flow needs to be adjusted. If you need > > more help, it is best to post a reproducible example, starting from > sample data available in the package. > > Hope that helps, > > Martin >> >> best, >> >> salih >> >> >> >> > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 8.2 years ago by Martin Morgan ♦♦ 23k
Answer: CGHcall and Normalization
0
gravatar for Salih Tuna
8.2 years ago by
Salih Tuna30
Salih Tuna30 wrote:
Thanks a lot Martin. That is very helpful. Best, salih -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: 13 June 2011 17:04 To: Salih Tuna Cc: bioconductor at r-project.org Subject: Re: [BioC] CGHcall and Normalization On 06/13/2011 08:01 AM, Salih Tuna wrote: > Hi Martin, > Thanks for your reply. I managed to run the code. AS you said I needed > to adjust the data. > But now the output seems something like this: > > normalized.data > cghRaw (storageMode: lockedEnvironment) > assayData: 3552 features, 5 samples > element names: copynumber > phenoData > sampleNames: AdCA10, SCC27, ..., SCC39 (5 total) > varLabels and varMetadata description: none > featureData > featureNames: RP11-465B22, RP4-785P20, ..., CTB-99K24 (3552 total) > fvarLabels and fvarMetadata description: > Chromosome: Chromosomal position > Start: Basepair position start > End: Basepair position end > experimentData: use 'experimentData(object)' > Annotation: > > This might be a very stupid question but I was expecting to see the > normalized data which is the same dimension as the raw data. I am sure I > can access the normalized data which is the same dimension as the raw > data. But I don't know how. Could you please show me how to do this? The docs for ?normalize say that the 'value' returned is a data.frame, but... class(normalized.data) tells me this is a cghRaw object (as does the display, above). So I looked at ?cghRaw and found that I could extract the copy number data with copynumber(normalized.data) And it seems to be different from (i.e., normalized) the raw data > example(CGHcall) [snip] > colSums(copynumber(raw.data)) AdCA10 SCC27 SCC32 SCC36 SCC39 -215.51938 46.58693 -153.71559 398.60994 518.95828 > colSums(copynumber(normalized.data)) AdCA10 SCC27 SCC32 SCC36 SCC39 -127.75115 -39.93650 -69.26762 134.13213 409.15257 so the documentation (also browseVignettes(package="CGHcall")) seems to be your friend (if a little difficult to navigate). Martin > > Best, > salih > > -----Original Message----- > From: Martin Morgan [mailto:mtmorgan at fhcrc.org] > Sent: 11 June 2011 16:24 > To: Salih Tuna > Cc: bioconductor at r-project.org > Subject: Re: [BioC] CGHcall and Normalization > > On 06/08/2011 08:47 AM, Salih Tuna wrote: >> Hi, >> >> i am trying to use the normalization function from CGHcall library. >> >> The command i use is >> >> >> >> normal.fullData<- normalize(fullData, method = "median", cellularity = >> 1) >> >> and i get the following error message. How can i solve this issue. >> >> Error in function (classes, fdef, mtable) : >> >> unable to find an inherited method for function "copynumber", for >> signature "data.frame" > > Hi Salih -- > > If I > > example(CGHcall) > > and look at how normalize() is used, the first argument is 'raw.data' > and it is > > > class(raw.data) > [1] "cghRaw" > attr(,"package") > [1] "CGHbase" > > if instead I > > > normalize(data.frame()) > Applying median normalization ... > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "copynumber", for > signature "data.frame" > > so perhaps you are trying to use a data.frame instead of an object of > 'cghRaw', i.e., your earlier work flow needs to be adjusted. If you need > > more help, it is best to post a reproducible example, starting from > sample data available in the package. > > Hope that helps, > > Martin >> >> best, >> >> salih >> >> >> >> > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
ADD COMMENTlink written 8.2 years ago by Salih Tuna30
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