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]]
> >
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> >
>
>
>


-- 


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

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