how to quickly find the corresponding sample of human in vitro comparing with that of rat in vitro for the given drug?

[Zhilong Jia]

Hello,

In terms of "Array Metadata.fixedchars.unix.csv", does the BARCODE items own some rule in naming the samples? how to quickly find the corresponding sample of human in vitro comparing with that of rat in vitro for the given drug at least to a certain extent?  Such only considering the durg without the dose and time.  I feel the data is a litter in disorder.

Another question: To the Preprocessed data, what actions have been done? 

Thank you.

[Djork-Arné Clevert]

Hi Zhi-Long,

the field "BARCODE" contains only the identifier for the CEL-file and does not provide any information about how to link drugs, concentrations and time-points across the different studies. I'm afraid, but you need to define your own mapping, e.g., rat in vivo 3hr corresponds to rat in vitro 2hr. It would be great, if you would share your mappings afterwards at this mailing list. 

The data preprocessing is described here: http://dokuwiki.bioinf.jku.at/doku.php/tgp_prepro?&#description_data_preprocessing

Let me know, if somethings is not clear.

Cheers,

Okko

-- 

Djork-Arné Clevert, PhD

Institute of Bioinformatics

Johannes Kepler University Linz

Phone: +49 30 4432 4702

Fax: +49 30 6883 5307

Email: ok...@clevert.de

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[Zhilong Jia]

Thank you for Dr. Clevert's reply.

I read the the described data preprocessing before. But I' confused that why the document "TGP Description" in the tgp info dir said that "Mas5 data ...". And http://dokuwiki.bioinf.jku.at/doku.php/contest_dataset (MAS5 data (folder) – it contains the MAS5 summarized array data; FARMS data (csv format) – contain the FARMS summarized array data). According to the  described preprocessing, it seems no Mas5 related in the preprocessed data, though I found the raw data dir includes a mas5 dir. 

About the mapping, If I've done, I'd like to share.

在 2013年4月9日星期二UTC+8下午7时56分31秒，Djork-Arné Clevert写道：

[Djork-Arné Clevert]

Hi Zhi-Long,

you are right the description is a bit imprecise regarding this issue. Therefore, I just have revised the download 

description. 

But coming back to your question: We provided the original data (registration is required to access this data)

which contains the cel-files and MAS5 summarized expression values. However, to facilitate data handling 

we also provide FARMS (http://bioinformatics.oxfordjournals.org/content/22/8/943.short) preprocessed 

data in CSV format. 

Please notice, that FARMS summarization clearly outperforms MAS5 with respect to sensitivity and specificity 

(see Affycomp Benchmark at http://affycomp.biostat.jhsph.edu/), this property allows for squeezing out more 

signal and might help improving the subsequent analysis.

Cheers,

Okko

-- 

Djork-Arné Clevert, PhD

Institute of Bioinformatics

Johannes Kepler University Linz

Phone: +49 30 4432 4702

Fax: +49 30 6883 5307

Email: ok...@clevert.de