2010/1/27 Mikhail <mikhail.dozmo...@gmail.com>:
> Henrik, thank you for such a thorough answer. Now I understand how to
> create two datasets, and it did work. I'm trying to use these datasets
> for FIRMAGene analysis, as described in
> http://bioinf.wehi.edu.au/folders/firmagene/sup3.R
> file. Nowhere in this file I can see how and where the two datasets
> are defined and compared. It starts with ONE dataset reading in cs,
>
> # this assumes the CEL files are at ./rawData/tissues/HuGene-1_0-st-
> v1/
> cs<-AffymetrixCelSet$fromName("tissues",cdf=cdf,verbose=verbose)
>
> and continues through FIRMAGene.
>
> Yes, I can create two datasets, as you described. Shall they be joined
> together to process for normalization and then to FIRMAGene? I tried
>
> csM <- AffymetrixCelSet$byName("MS", tags="M", cdf=cdf)
> csS <- AffymetrixCelSet$byName("MS", tags="S", cdf=cdf)
>
> cs<-cbind(csM,csS)
Now I'm starting to understanding your question better. You want to
keep the data sets in different directories (as solved), but join them
together into one for the analysis. In order to do this, you can
append one set to another. The safest/best way to do this would be to
do:
cs <- append(csM, csS);
setFullName(cs, "MS,M+S");
This will setup a set of your 3+3 CEL files with fullname "MS,M+S".
This name will be used in all downstream analysis/output data sets.
If you don't use setFullName(), the fullname will be that of the first
data set ('csM').
/Henrik
>
> Is it correct? I doubt, because the following code in the example
> file mentioned above doesn't work. I wonder if FIRMAGene can
> recognize the tags from two datasets, for proper comparison. There are
> several example files at http://bioinf.wehi.edu.au/folders/firmagene/,
> none of them, however, explains where datasets for comparison are
> defined. Therefore I wonder which directory structure shall I create
> and how to properly read the data for FIRMAGene processing.
>
> Originally, I have 3 .cel files for one condition (M), and 3 .cel
> files for another (S). Thank you! Mikhail.
>
> On Jan 26, 6:58 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
> wrote:
>> Hi
>>
>> On Tue, Jan 26, 2010 at 3:32 PM, Mikhail <mikhail.dozmo...@gmail.com> wrote:
>> > Hi,
>> > Onhttp://www.aroma-project.org/node/79there's nice summary of what
>> > the directory structure should look like. To my understanding the
>> > directory structure also reflects the project structure.
>>
>> The annotationData/chipTypes/ directory structure shouldn't. Image
>> that this as a global structure shared with everyone.
>>
>> > For example,
>> > I want to identify differentially expressed exons from Affymetrix
>> > Human Gene 1.0 ST, using
>> > FIRMAgenehttp://bioinf.wehi.edu.au/folders/firmagene/.
>> > I have two groups, and need to compare them. So I set the structure
>> > like this:
>>
>> > For annotation:
>> > annotationData\chipTypes\HuGene-1_0-st-v1
>> > annotationData\chipTypes\HuGene-1_0-st-v1\HuGene-1_0-st-v1_M
>> > annotationData\chipTypes\HuGene-1_0-st-v1\HuGene-1_0-st-v1_S
>>
>> Not sure what you mean by two "groups" in this context and what 'M'
>> and 'S' refers to. Are those two latter subdirectories?
>>
>> Note that the definition of a 'chip type' differ from the definition
>> of an annotation data file (e.g. CDF file). The chip type never
>> changes after the array is designed and produced by Affymetrix. The
>> annotation data files will change as the human genome annotation and
>> other things gets updated.
>>
>> Thus, if you buy HuGene-1_0-st-v1 arrays from Affymetrix, you want any
>> annotation data files to be stored under
>> annotationData/chipTypes/HuGene-1_0-st-v1/. Similarly, for you raw
>> data files.
>>
>> Let's see if my below comments clarifies it to you.
>>
>>
>>
>> > For rawData:
>> > rawData\MS
>> > rawData\MS\HuGene-1_0-st-v1_M
>> > rawData\MS\HuGene-1_0-st-v1_S
>>
>> I believe you want to do:
>>
>> rawData/MS,M/HuGene-1_0-st-v1/
>> rawData/MS,S/HuGene-1_0-st-v1/
>>
>> This way you will have two data sets for the same chip type with
>> fullnames "MS,M" and "MS,S". By definition of names, tags &
>> fullnames, both data sets have the name "MS" differing by the tags "M"
>> and "S".
>>
>> You can also use fullnames "MS_M" and "MS_S", which then gives data
>> sets with different names (same) and no tags.
>>
>>
>>
>> > The following code runs OK
>> > chipType <- "HuGene-1_0-st-v1"
>> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>>
>> So, I'm not sure where you placed the CDF, but yes, the CDF will be
>> found if it is located in (or in a subdirectory of)
>> annotationData/chipTypes/HuGene-1_0-st-v1/.
>>
>>
>>
>> > But this
>> > cs <- AffymetrixCelSet$byName("MS", cdf=cdf)
>> > gives an error:No such directory: MS/HuGene-1_0-st-v1
>>
>> > I don't want to put all my files in the same HuGene-1_0-st-v1 folder,
>> > they are from different groups and suppose to be compared.
>>
>> Using the rawData/ structure I suggest above, you can do:
>>
>> csM <- AffymetrixCelSet$byName("MS", tags="M", cdf=cdf)
>> csS <- AffymetrixCelSet$byName("MS", tags="S", cdf=cdf)
>>
>> or equivalently
>>
>> csM <- AffymetrixCelSet$byName("MS,M", cdf=cdf)
>> csS <- AffymetrixCelSet$byName("MS,S", cdf=cdf)
>>
>> If you then process:
>>
>> cs <- csM
>>
>> all output data sets will have prefix "MS,M" with additional tags
>> added. Analogously for 'csS'.
>>
>> > Besides, my
>> > folder structure reflects the one
>> > describedhttp://www.aroma-project.org/node/79.
>> > How do I solve it? If not via directory structure, is there a file
>> > where I can specify which .cel file belongs to which group? Thank you.
>>
>> No, on purpose we do not provide ways to specify data sets/files via a
>> file. This is because we want to keep the setup options to one
>> standard; the more options there are the more confusions there will be
>> and the harder it will be to troubleshoot and share scripts etc.
>>
>> Hope this helps
>>
>> Henrik
>>
>>
>>
>>
>>
>> > --
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>
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