Thanks Tom. I think I misunderstood the experiment design here for pair
data. As you said, the experiment design was :
 Samples Patients Tissue Response  1 1   Normal Y  2 2     Normal Y  3  3
         Normal N  4 4   Normal N  5 1   Tumor Y  6 2   Tumor Y  7 3
Tumor N  8 4   Tumor N
Now I can understand you said in this situation. The result: topCounts(pairCD,
group = 2) focused on the difference between Response Y and Response N.
And if I want to compare the difference between Normal and Tumor, I need to
use: topCounts(pairCD, group = 1)

But in my experiment, there are no "Response", How can I write the
new("pairedData")
command if I just want to compare the difference between Normal and Tumor?
Thank you!

Best,
Shilin



2014-02-12 4:19 GMT-06:00 Tom Hardcastle <tjh48@cam.ac.uk>:

>  Hi Shilin,
>
> The confusion is in the groups. Data columns 1-4 are paired with columns
> 5-8 respectively, as you have identified. However, there is a further
> structure to the data, which is that the first two paired samples are
> biologically distinct from the second two paired samples. Replicate group 1
> is thus 159:73, 44:24, and replicate group 2 is 0:49, 0:68 - the groups are
> defined on the *paired* data. This situation might arise, for example, if
> the first two pairings consist of normal and tumour tissue from patients
> responding to treatment, and the second two normal and tumour tissue
> patients from non-responders. The replicate structure 'c(1,1,2,2)' and the
> DE group is designed to describe this structure - the first two pairings
> are distinct from the second two pairings.
>
> The DE analysis (correctly) identifies that there is a large and
> consistent difference in ratio between the two groups - in the first group,
> the data are 159:73 and 44:24, so the first member of each pair is
> approximately twice that of the second member; in the second group, the
> data are 0:49 and 0:68, so the first member of each pair is substantially
> less than that of the second member.
>
> If the question you would like to answer is 'where are there consistent
> differences between the paired data', rather than 'where are there
> consistent differences in the ratios of paired data between replicate
> groups', you can use the nullProps = 0.5 option as given in the vignette,
> and look at the topCounts table for the non-differentially expressed
> (between replicates) data (page 9 of the vignette).
>
> Hope that helps,
>
> Tom
>
>
> ------- Original Message --------  Subject: [BioC] Paired Data Analysis
> in baySeq package  Date: Wed, 12 Feb 2014 00:14:44 -0600  From: zhao
> shilin <zhaoshilin@gmail.com> <zhaoshilin@gmail.com>  To:
> bioconductor@r-project.org <bioconductor@r-project.org><bioconductor@r-project.org>
>
> Hi all,
>
> Is there anybody who is familiar with the Paired Data Analysis in baySeq
> package. I'm following the instructions in its vignette. I used:
>
> library(baySeq)
> data(pairData)
> pairCD <- new("pairedData", data = pairData[,1:4], pairData =
> pairData[,5:8],replicates = c(1,1,2,2),groups = list(NDE = c(1,1,1,1), DE =
> c(1,1,2,2)))
>
> As it indicated, The first four columns in these data are paired with the
> second four columns. So I think Sample 1-Sample 4 is group1 and Sample
> 5-Sample 8 is group2. And Sample 1 is paired with Sample 5, Sample 2 is
> paired with Sample 6~~~
> In the result, the most significant gene is the 5th row.  The result is:
>
>    rowID   X1.1  X1.2     X2.1   X2.2 Likelihood  DE      FDR.DE
>
> 1      5 159:73 44:24     0:49   0:68  0.9974276 1>2 0.002572417
>
> Its expression is:
> 159  44   0   0  73  24  49  68
>
> It is very obvious that the software take 3th and 4 th samples (0,0) as
> group 2, 7th and 8th samples (49, 68) as group 1, which is not correct.
> So I am not very clear with the replicates = c(1,1,2,2) and DE =
> c(1,1,2,2). What do they mean here? What is the correct method to do paired
> data analysis in baySeq package?
>
> Thank you!
>
> Best,
> Shilin
>
> 	[[alternative HTML version deleted]]
>
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>
>
>
>
>
> --
> Dr. Thomas J. Hardcastle
>
> Department of Plant Sciences
> University of Cambridge
> Downing Street
> Cambridge, CB2 3EA
> United Kingdom
>
>

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