[BioC] HTqPCR

[Heidi Dvinge]

Hi Bingbing,

> Hi Heidi,
> We downloaded the R-devel version, and all the functions and sample
> fluidigm_sample.csv is included. Thank you!

Glad you got it to work.

> I have 2 samples of 96x96 fluidigm data. How can I display the layout of
> the qPCR in the 2nd sample?

In order to plot each array individually, you'll have to apply
changeCtLayout to each of the 2 samples in your qPCRset individually.
Otherwise you'll get an object of other dimensions that yu probably
expect. E.g.:

> # Locate test dta
> exPath <- system.file("exData", package="HTqPCR")
> exFiles <- "fluidigm_sample.csv"
>
> # Create qPCRset object
> # Reading is same file twice, to pretend to have multiple samples
> temp	<- readCtData(c(exFiles, exFiles), path=exPath, n.features=48*48,
flag=9, feature=5, type=6, Ct=7, position=1, skip=12, sep=",")
>
> # Re-format data, to contain n.features individual genes
> all.raw <- changeCtLayout(temp, sample.order=rep(1:48, each=48))
> all.raw
An object of class "qPCRset"
Size:  48 features, 96 samples
Feature types:		 Test
Feature names:		 b actin b actin b actin ...
Feature classes:
Feature categories:	 OK
Sample names:		 1:fluidigm_sample 1:fluidigm_sample 2:fluidigm_sample ...

On my two arrays I have a total of 96 samples (or 2x96 in your case for
the different dimension of the Fluidigm array). Hence, the final qPCRset
object will have 96 columns, since these are considered to be all the
individual samples that will be tested for differential expression further
downstream.

In order to process each of your original Fluidigm cards individually, you
can say:

> # Process each sample individually
> for (n in 1:n.samples(temp)) {
+ 	# Re-format from 1x2304 samples in input file into 48x48 as on array
+ 	raw	<- changeCtLayout(temp[,n], sample.order=rep(1:48, each=48))
+ 	# Plot
+ 	plotCtArray(raw, main=paste("Sample ", n, ": ", sampleNames(temp)[n]))
+ }

You'd probably want to write that to a file, or open a new window for each
plot, but that's the general approach.

Please let me know if this doesn't work.
\Heidi


>
> Here is my qPCRset
>> temp <- readCtData(path="data/4HTqPCR", file=files$File, n.features =
>> 96*96, flag=5, feature=3, type=4, Ct=2, position =1, sep = "\t")
>
>>temp
> An object of class "qPCRset"
> Size:  9216 features, 2 samples
> Feature types:           S01, S02, S03, S04, S05, S06, S07, S08, S09, S10,
> S11, S12, S13, S14, S15, S16, S17, S18, S19, S20, S21, S22, S23, S24, S25,
> S26, S27, S28, S29, S30, S31, S32, S33, S34, S35, S36, S37, S38, S39, S40,
> S41, S42, S43, S44, S45, S46, S47, S48, S49, S50, S51, S52, S53, S54, S55,
> S56, S57, S58, S59, S60, S61, S62, S63, S64, S65, S66, S67, S68, S69, S70,
> S71, S72, S73, S74, S75, S76, S77, S78, S79, S80, S81, S82, S83, S84, S85,
> S86, S87, S88, S89, S90, S91, S92, S93, S94, S95, S96
> Feature names:           control1 control1 control2 ...
> Feature classes:
> Feature categories:      Undetermined, OK
> Sample names:            sample1 sample2 NA ...
>
>
>> raw <- changeCtLayout(temp, sample.order = rep(1:96, each = 96))
>> plotCtArray(raw)
>
>> raw2 <- changeCtLayout(temp, sample.order = rep(97:192, each = 96))
>> plotCtArray(raw2)
>
> but, plotCtArray(raw) gave the same layout as plotCtArray(raw2)
>
>
> Thanks,
> Bingbing
>
>
>
>
>
>
>
>
>
> ----- Original Message -----
> From: "Heidi Dvinge" <heidi at ebi.ac.uk>
> To: "Bingbing Yuan" <byuan at wi.mit.edu>
> Sent: Thursday, September 1, 2011 2:09:12 AM
> Subject: Re: HTqPCR
>
> Hi Bingbing,
>
> what version of HTqPCR do you have? The Fluidigm-related functions are
> relatively newly added. What's your output of sessionInfo()
>
> The current version is 1.7.3, c.f.
> http://www.bioconductor.org/packages/devel/bioc/html/HTqPCR.html This is
> technically for the R-devel version, i.e. 2.14, but I'm running it myself
> on 2.13 without any issues so far. In that case you can't install it with
> biocLite though, but will have to download it from the webpage above, and
> install it manually.
>
> Cheers
> \Heidi
>
>
>> Hi Heidi,
>> Thanks a lot for quick reply.
>> In the package that we downloaded, there is no function of
>> plotCtVariation
>> and plotCtArray. Any idea?
>> Thanks,
>> Bingbing
>>
>>
>> ----- Original Message -----
>> From: "Heidi Dvinge" <heidi at ebi.ac.uk>
>> To: "Bingbing Yuan" <byuan at wi.mit.edu>
>> Sent: Wednesday, August 31, 2011 1:52:28 PM
>> Subject: Re: HTqPCR
>>
>> Hi Bingbing,
>>
>> my apologies, the file should be attached here. I'll make sure it's
>> added
>> to future HTqPCR releases.
>>
>> Best wishes
>> \Heidi
>>
>>> Dear Heidi,
>>> We downloaded the HTqPCR ( Release 2.8 ) from bioconductor this week,
>>> and
>>> fluidigm_sample.csv is not in the HTqPCR/exData/ folder. Could you
>>> direct
>>> me or send me this example file?
>>> Thanks,
>>> Bingbing
>>>
>>>
>>> --
>>> Bingbing Yuan M.D. Ph.D.
>>> Bioinformatics Scientist
>>> Whitehead Institute for Biomedical Research
>>> tel: 617 258 6109
>>> byuan at wi.mit.edu
>>>
>>
>> --
>> Bingbing Yuan M.D. Ph.D.
>> Bioinformatics Scientist
>> Whitehead Institute for Biomedical Research
>> tel: 617 258 6109
>> byuan at wi.mit.edu
>>
>
>
>
> --
> Bingbing Yuan M.D. Ph.D.
> Bioinformatics Scientist
> Whitehead Institute for Biomedical Research
> tel: 617 258 6109
> byuan at wi.mit.edu
>