Error: read.affybatch
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S Peri ▴ 320
@s-peri-835
Last seen 9.6 years ago
Hello group, I am trying to read my cel files using read.affybatch method. I stored all my cel files, probe information file and experiment file in one directory. I used the following commands: >fls = list.files() >ab = read.affybatch(filenames=fls) Error in initialize(value, ...) : Is breastCancerData_2.txt really a CEL file? tried reading as text, gzipped text and binary In addition: Warning message: Incompatible phenoData object. Created a new one. in: read.affybatch(filenames = fls) I am getting the above error. What could be happening. I am trying to analyze Mike West and Nievens Breast cancer affy data (Duke University). Could any one please help me what is wrong here and also how does a phenoData file look like. What is phenoData. Please help. thank you SP
probe affy probe affy • 1.5k views
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S Peri ▴ 320
@s-peri-835
Last seen 9.6 years ago
After reading a ?read.phenoData I tried the following: > read.phenoData(filename = "Cel_key.txt") Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 3 did not have 7 elements cel_key.txt file looks like this: CEL file name ER status LN status Nevins4 pos pos Nevins5 pos pos Nevins6 pos pos Nevins7 neg pos Nevins8 neg pos Nevins9 neg pos Nevins11 neg pos Nevins13 pos pos Nevins19 pos pos Nevins20 pos pos Nevins21 pos neg Nevins22 pos neg Nevins23 neg neg Nevins24 neg neg Nevins25 neg neg Nevins26 neg neg Nevins36 pos neg Nevins37 pos neg Nevins38 pos neg Nevins39 pos neg Nevins40 pos pos Nevins41 pos pos Nevins42 neg neg Nevins43 neg neg Nevins46 pos pos Nevins47 neg pos Nevins48 neg neg Nevins97 neg neg Nevins98 neg pos thanks SP --- S Peri <biocperi@yahoo.com> wrote: > Hello group, > I am trying to read my cel files using > read.affybatch > method. > > I stored all my cel files, probe information file > and > experiment file in one directory. > > I used the following commands: > > >fls = list.files() > >ab = read.affybatch(filenames=fls) > Error in initialize(value, ...) : Is > breastCancerData_2.txt really a CEL file? tried > reading as text, gzipped text and binary > In addition: Warning message: > Incompatible phenoData object. Created a new one. > in: read.affybatch(filenames = fls) > > > I am getting the above error. What could be > happening. > I am trying to analyze Mike West and Nievens Breast > cancer affy data (Duke University). > > Could any one please help me what is wrong here and > also how does a phenoData file look like. What is > phenoData. > > Please help. > > thank you > > SP > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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S Peri ▴ 320
@s-peri-835
Last seen 9.6 years ago
hi Ben, All my CEL files are with .CEL extension. They are not text files. When I open them they are exactly in the same format as CEL (starting with [CEL] header). In addition to all the CEL files in the directory I have all my CEL files, I had two other files with names Cel_key.xls and breastCancerData_2.xls which I changed them to Cel_key.txt and breastCancerData_2.txt(both as tab delimited txt files). Pls. suggest what I am doing wrong. Thanks SP --- Ben Bolstad <bolstad@stat.berkeley.edu> wrote: > how come your cel files end in .txt? are you sure > they are cel files > and not something else? What do you see if you open > up one of the files. > > Also, for most people ReadAffy() is a better way > then calling > read.affybatch() since it will create the phenodata > automatically. > > Ben > > > > > > On Wed, 2004-06-30 at 20:38, S Peri wrote: > > Hello group, > > I am trying to read my cel files using > read.affybatch > > method. > > > > I stored all my cel files, probe information file > and > > experiment file in one directory. > > > > I used the following commands: > > > > >fls = list.files() > > >ab = read.affybatch(filenames=fls) > > Error in initialize(value, ...) : Is > > breastCancerData_2.txt really a CEL file? tried > > reading as text, gzipped text and binary > > In addition: Warning message: > > Incompatible phenoData object. Created a new one. > > in: read.affybatch(filenames = fls) > > > > > > I am getting the above error. What could be > > happening. > > I am trying to analyze Mike West and Nievens > Breast > > cancer affy data (Duke University). > > > > Could any one please help me what is wrong here > and > > also how does a phenoData file look like. What is > > phenoData. > > > > Please help. > > > > thank you > > > > SP > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- > Ben Bolstad <bolstad@stat.berkeley.edu> > http://www.stat.berkeley.edu/~bolstad > >
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Try either myData <- ReadAffy() or myData <- read.affybatch(files=list.celfiles()) Thanks, Ben On Wed, 2004-06-30 at 21:16, S Peri wrote: > hi Ben, > > All my CEL files are with .CEL extension. They are not > text files. When I open them they are exactly in the > same format as CEL (starting with [CEL] header). > > In addition to all the CEL files in the directory I > have all my CEL files, I had two other files with > names Cel_key.xls and breastCancerData_2.xls which I > changed them to Cel_key.txt and > breastCancerData_2.txt(both as tab delimited txt > files). > > Pls. suggest what I am doing wrong. > > Thanks > SP > > --- Ben Bolstad <bolstad@stat.berkeley.edu> wrote: > > how come your cel files end in .txt? are you sure > > they are cel files > > and not something else? What do you see if you open > > up one of the files. > > > > Also, for most people ReadAffy() is a better way > > then calling > > read.affybatch() since it will create the phenodata > > automatically. > > > > Ben > > > > > > > > > > > > On Wed, 2004-06-30 at 20:38, S Peri wrote: > > > Hello group, > > > I am trying to read my cel files using > > read.affybatch > > > method. > > > > > > I stored all my cel files, probe information file > > and > > > experiment file in one directory. > > > > > > I used the following commands: > > > > > > >fls = list.files() > > > >ab = read.affybatch(filenames=fls) > > > Error in initialize(value, ...) : Is > > > breastCancerData_2.txt really a CEL file? tried > > > reading as text, gzipped text and binary > > > In addition: Warning message: > > > Incompatible phenoData object. Created a new one. > > > in: read.affybatch(filenames = fls) > > > > > > > > > I am getting the above error. What could be > > > happening. > > > I am trying to analyze Mike West and Nievens > > Breast > > > cancer affy data (Duke University). > > > > > > Could any one please help me what is wrong here > > and > > > also how does a phenoData file look like. What is > > > phenoData. > > > > > > Please help. > > > > > > thank you > > > > > > SP > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > > Ben Bolstad <bolstad@stat.berkeley.edu> > > http://www.stat.berkeley.edu/~bolstad > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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Hello group, I am trying to normalize using expresso module and I am getting the following error. In fact I followed the example given at the bottom of help file. The following is what I get: > abcel.data.norm = expresso(abcel.data, bgcorrect.method = "rma", normalize.method = "constant", pmcorrect.method = "pmonly", summary.method = "avgdiff") background correction: rma normalization: constant PM/MM correction : pmonly expression values: avgdiff background correcting...Error in bg.correct(afbatch, method = bgcorrect.method) : No direct or inherited method for function "bg.correct" for this call Any suggestions where it is going wrong. Thank you. SP
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Yes all your CEL files may end with .CEL extension. But look at the first line of your code : > > > >fls = list.files() So fls will contain the filenames of all files including .txt and other extensions (as you have already mentioned that you stored everything in one folder). So try using list.celfiles() or simply ReadAffy() or try this : list.files(pattern=".CEL") PS: Please use the assignment operator "<-" instead of "=" . On Thu, 2004-07-01 at 05:16, S Peri wrote: > hi Ben, > > All my CEL files are with .CEL extension. They are not > text files. When I open them they are exactly in the > same format as CEL (starting with [CEL] header). > > In addition to all the CEL files in the directory I > have all my CEL files, I had two other files with > names Cel_key.xls and breastCancerData_2.xls which I > changed them to Cel_key.txt and > breastCancerData_2.txt(both as tab delimited txt > files). > > Pls. suggest what I am doing wrong. > > Thanks > SP > > --- Ben Bolstad <bolstad@stat.berkeley.edu> wrote: > > how come your cel files end in .txt? are you sure > > they are cel files > > and not something else? What do you see if you open > > up one of the files. > > > > Also, for most people ReadAffy() is a better way > > then calling > > read.affybatch() since it will create the phenodata > > automatically. > > > > Ben > > > > > > > > > > > > On Wed, 2004-06-30 at 20:38, S Peri wrote: > > > Hello group, > > > I am trying to read my cel files using > > read.affybatch > > > method. > > > > > > I stored all my cel files, probe information file > > and > > > experiment file in one directory. > > > > > > I used the following commands: > > > > > > >fls = list.files() > > > >ab = read.affybatch(filenames=fls) > > > Error in initialize(value, ...) : Is > > > breastCancerData_2.txt really a CEL file? tried > > > reading as text, gzipped text and binary > > > In addition: Warning message: > > > Incompatible phenoData object. Created a new one. > > > in: read.affybatch(filenames = fls) > > > > > > > > > I am getting the above error. What could be > > > happening. > > > I am trying to analyze Mike West and Nievens > > Breast > > > cancer affy data (Duke University). > > > > > > Could any one please help me what is wrong here > > and > > > also how does a phenoData file look like. What is > > > phenoData. > > > > > > Please help. > > > > > > thank you > > > > > > SP > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > > Ben Bolstad <bolstad@stat.berkeley.edu> > > http://www.stat.berkeley.edu/~bolstad > > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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