HTqPCR
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wenhuo hu ▴ 200
@wenhuo-hu-5208
Last seen 3.6 years ago
United States
Hi everyone, I am using HTqPCR package. After I updated to 1.10.0 version, the function readCtData() is not working as before: readCtData('borig.csv', header=F, n.features = 768, feature=6, position=1, Ct=11, path="./orig") -> raw; while if I do this: readCtData('borig.csv', header=F, n.features = 768, path="./orig", format='plain') -> raw; at the same time, put the feature at 6th col, position at 3rd col, Ct at 8th col. It works. But all my data has the old settings. So, is there anyway to change this HTqPCR to fit my older format data? Thanks. Wenhuo [[alternative HTML version deleted]]
HTqPCR HTqPCR • 872 views
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 7.4 years ago
Hi Wenhuo, > Hi everyone, > > I am using HTqPCR package. After I updated to 1.10.0 version, the function > readCtData() is not working as before: > readCtData() was changed in version 1.10.0 to accommodate more different input formats, depending on the vendor of the qPCR assay. Some more examples are given in the vignette. Before, the default behaviour was to read in the following columns: flag=4, feature=6, type=7, position=3, Ct=8. If you select format="plain", these columns will still be accessed, hence the default behaviour of readCtData() hasn't changed between previous versions of HTqPCR and the most current one. Therefore, I'm not entirely sure what you mean when you say that all your data has the 'old settings'. Can you perhaps describe the column content and/or file header? If your information is listed in different columns, you can change your preference using the column.info=list() argument. For example: raw <- readCtData('borig.csv', header=F, n.features = 768, column.info=list(feature=6, position=1, Ct=11), path="./orig") Using your example ought to give you an error message something long the lines of: > readCtData('borig.csv', header=F, n.features = 768, feature=6, position=1, Ct=11, path="./orig") -> raw; Warning message: In readCtData('borig.csv', header=F, n.features = 768, feature=6, position=1, Ct=11, path="./orig") : Please use 'column.info' for providing a list of column numbers containing particular information. The use of 'flag', 'feature', 'type', 'position' and 'Ct' is deprecated and will be removed in future versions. HTH \Heidi > readCtData('borig.csv', header=F, n.features = 768, feature=6, position=1, > Ct=11, path="./orig") -> raw; > > while if I do this: > readCtData('borig.csv', header=F, n.features = 768, path="./orig", > format='plain') -> raw; > > at the same time, put the feature at 6th col, position at 3rd col, Ct at > 8th col. It works. But all my data has the old settings. So, is there > anyway to change this HTqPCR to fit my older format data? > > Thanks. > > Wenhuo > > [[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 >
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Hi Heidi, Thank you so much. It works very nicely with the column.info. Perfect! Wenhuo Hu On Tue, Apr 24, 2012 at 11:22 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote: > Hi Wenhuo, > > > Hi everyone, > > > > I am using HTqPCR package. After I updated to 1.10.0 version, the > function > > readCtData() is not working as before: > > > readCtData() was changed in version 1.10.0 to accommodate more different > input formats, depending on the vendor of the qPCR assay. Some more > examples are given in the vignette. > > Before, the default behaviour was to read in the following columns: > flag=4, feature=6, type=7, position=3, Ct=8. If you select format="plain", > these columns will still be accessed, hence the default behaviour of > readCtData() hasn't changed between previous versions of HTqPCR and the > most current one. Therefore, I'm not entirely sure what you mean when you > say that all your data has the 'old settings'. Can you perhaps describe > the column content and/or file header? > > If your information is listed in different columns, you can change your > preference using the column.info=list() argument. For example: > > raw <- readCtData('borig.csv', header=F, n.features = 768, > column.info=list(feature=6, position=1, Ct=11), path="./orig") > > Using your example ought to give you an error message something long the > lines of: > > readCtData('borig.csv', header=F, n.features = 768, feature=6, > position=1, > Ct=11, path="./orig") -> raw; > Warning message: > In readCtData('borig.csv', header=F, n.features = 768, feature=6, > position=1, Ct=11, path="./orig") : > Please use 'column.info' for providing a list of column numbers > containing particular information. The use of 'flag', 'feature', 'type', > 'position' and 'Ct' is deprecated and will be removed in future > versions. > > HTH > \Heidi > > > readCtData('borig.csv', header=F, n.features = 768, feature=6, > position=1, > > Ct=11, path="./orig") -> raw; > > > > while if I do this: > > readCtData('borig.csv', header=F, n.features = 768, path="./orig", > > format='plain') -> raw; > > > > at the same time, put the feature at 6th col, position at 3rd col, Ct at > > 8th col. It works. But all my data has the old settings. So, is there > > anyway to change this HTqPCR to fit my older format data? > > > > Thanks. > > > > Wenhuo > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- Wenhuo Hu Park lab Memorial Sloan Kettering Cancer Center Zuckerman Research Building 408 East 69th Street Room ZRC-527 New York, NY 10065 Phone 646-888-3220 huw@mskcc.org [[alternative HTML version deleted]]
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