[BioC] HTqPCR

[Heidi Dvinge]

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
>
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>
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