[BioC] qPCRnorm

[Heidi Dvinge]

Hello Andreia,

sure, if you want to remove some of the data points in HTqPCR you can  
use the function filterCtData(). If featureType of your genes are  
e.g. "Endogenous Control" and "Target", you can remove all the target  
genes; filterCtData(qPCRset, remove.type=c("Target")). See ? 
filterCtData for more examples.

Note that for many of the plotting functions this is actually not  
necessary, since you can automatically stratify the data based on  
various feature characteristics. If you're interested in different  
featureType() or featureClass(), you can for example say plotCtBoxes 
(qPCRset, stratify="type") or with stratify="class". For other plot  
types, such as scatter plots, features can be coloured differently  
depending on featureType or some other characteristics; e.g.  
plotCtScatter(qPCRset, col="type").

Cheers
\Heidi


On 11 Jan 2010, at 16:37, Andreia Fonseca wrote:

> Hello Heidi,
>
> thanks for the code, until now everything seems to be o.k. I am  
> trying to filter data and I was wondering if you have created  
> functions to select data, the reason is that I want to plot the Ct  
> values just for the endogenous control targets to see if there are  
> significant differences between treatments, something like  
> select.type??
> Cheers
> Andreia
>
> On Fri, Jan 8, 2010 at 4:45 PM, Heidi Dvinge <heidi at ebi.ac.uk> wrote:
> Hello Andreia,
>
> I've attached a file with all the latest source code. I still need  
> to add
> some things plus delete other and correct the documentation, before I
> compile it together into a package. However, in your case it should  
> work
> if you say:
>
> > library(HTqPCR)   # To get the vignette and help files available
> > source("where.ever.you.place.the.file/source_functions_v1.1.1.R") #
> Overwrite old functions with corrected ones.
>
> I don't have access to a windows machine right now so I can't test  
> it, but
> if you still get errors when you try to run through the vignette, then
> drop me a line. The sooner I get bugs corrected, the better :)
>
> Cheers
> \Heidi
>
> > Hi Heidi,
> >
> > can you send me the sample data file, this way I can read it  and
> > continue.
> > cheers
> > Andreia
> >
> > On Fri, Jan 8, 2010 at 11:37 AM, Heidi Dvinge <heidi at ebi.ac.uk>  
> wrote:
> >
> >> Hi Andreia,
> >>
> >> well, sadly enough that's because I'm a numpty!! When I wrote the
> >> function(s), rather than defining file position using file.path,  
> I just
> >> concatenated names with "/" because at that point I was only  
> intending
> >> on
> >> using this function for myself on my mac.
> >>
> >> On mac/linux this can be fixed for readCtData by having the data  
> you
> >> want
> >> to read in a different directory than your current working  
> directory.
> >> However, for windows you'll need a bug-fixed version of  
> readCtData(). I
> >> have this available, but it hasn't been submitted to the BioC devel
> >> repository yet - it's creeping rapidly higher up on my to-do  
> list. If
> >> you
> >> want, I can send you a version off-list.
> >>
> >> Cheers
> >> \Heidi
> >>
> >> > Hi Heidi,
> >> >
> >> > Thanks for the advise. I am going through the HTqPCR  
> documentation but
> >> I
> >> > am
> >> > getting the following error while trying to read the sample input
> >> data:
> >> >
> >> > path <- system.file("exData", package = "HTqPCR")
> >> >> head(read.delim(file.path(path, "files.txt")))
> >> > Error in file(file, "r") : cannot open the connection
> >> > In addition: Warning message:
> >> > In file(file, "r") :
> >> >   cannot open file '/files.txt': No such file or directory
> >> >> files <- read.delim(file.path(path, "files.txt"))
> >> > Error in file(file, "r") : cannot open the connection
> >> > In addition: Warning message:
> >> > In file(file, "r") :
> >> >   cannot open file '/files.txt': No such file or directory
> >> >
> >> >
> >> > I am working in a windows machine and using R 2.9.2
> >> >
> >> > thanks
> >> > Andreia
> >> >
> >> > On Fri, Jan 8, 2010 at 8:44 AM, Heidi Dvinge <heidi at ebi.ac.uk>  
> wrote:
> >> >
> >> >> Hello Andreia,
> >> >>
> >> >> I'm not familiar with qpcrBatch objects, but <shameless self  
> plug> if
> >> >> you're interested in testing for differential expression between
> >> genes,
> >> >> you could also consider the HTqPCR package. The raw data is  
> read into
> >> a
> >> >> qPCRSet object, which is similar to ExpressionSets used for
> >> microarray
> >> >> data. The package performs various normalisations of the raw  
> qPCR
> >> data,
> >> >> similar to qpcrNorm, along with some data visualisation and
> >> filtering.
> >> >> Differential expression can be analysed using a standard t- 
> test or
> >> with
> >> >> a
> >> >> limma-based approach, or if you want to do something else  
> than that
> >> you
> >> >> can extract all the values from your qPCRSet object using  
> exprs().
> >> >> </shameless self plug>
> >> >>
> >> >> Cheers
> >> >> \Heidi
> >> >>
> >> >> > Dear list,
> >> >> >
> >> >> > I am trying to understand how qpcrNorm works, so I followed  
> the
> >> >> > documentation, so I understood how to normalize the data,  
> but now I
> >> >> want
> >> >> > to
> >> >> > test which genes are differentially expressed between  
> batches and
> >> make
> >> >> a
> >> >> > Mann-Whitney U-test. How can I transform the normalized  
> data which
> >> is
> >> >> a
> >> >> > object class qpcrBatch into a data.frame. Or else how can test
> >> using
> >> >> this
> >> >> > kind of object.
> >> >> > Thanks for the help
> >> >> > Andreia
> >> >> >
> >> >> >       [[alternative HTML version deleted]]
> >> >> >
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