Cytoscan HD array

[Charles Mullighan]

Dear Cheng
Can dChip process the new Cytoscan HD arrays from affy, or if not, can
it be modified to do so?
Charles

[Cheng Li]

Hi Charles,

We are testing dchip on this new array type. Please see some notes below and let me know how it goes.

Thank you.

Cheng

-- Select "SNP 6.0" at "Analysis/Open group/Other info/Array type".

-- At "Analysis/Model", please try the "Average" option.

-- Try the code here (note 2/23/10) to make genome info files from Annotation CSV files.
https://sites.google.com/site/dchipsoft/snp-array-analysis/snp-array-data-processing/genome-information-files-for-snp-arrays

Charles

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[Charles Mullighan]

Dear Cheng

When running large batches of SNP6 chips, a couple of issues:

If there are too many values for Refbatch, then dChip doesn't recognize that column at all.

For other variables (e.g. MRN, U133A ID) it is nice to have those shown in the SI file, but if there are too many values dChip throws an error.

Also, there is function to "get external data" and "update sample information file" but on doing so, dChip hangs and crashes.

Can these features be altered/fixed?

Charles

[Monica Messina]

Dear Cheng,

 

I am experiencing some problem in generating the genome info for cytoscan arrays. Can you provide the script to generate it by Python or the file itself?

 

Thank you for your help,

 

Monica

[Cheng Li]

Monica,

Can you try a quick solution: copy and paste columns from Affy CSV files to resemble a dchip genome info file (save in tab-delimited text format):
https://sites.google.com/site/dchipsoft/snp-array-analysis/view-data-along-chromosome/genome-information-file

Cheng
www.ChengLiLab.org

[Monica Messina]

Dear Cheng,

 

I created a txt file from the CSV, as you suggested, including only the columbs required in the genome info but it doesn't work in dChip.

 

Thus, I went back to the Python script but I always get this error:

 

File "C:\Users\monica\Documents\Annotation files\Cytoscan_mod_monica\cytoscan_genome_info_SNP_2.7.py", line 48, in <module>
    if words[1] in info:
IndexError: list index out of range

 

It seems as it is not able to join the csv and cdf files. Do you know whether the cdf is correct and it is the correct extension of the file or it would be better to provide a psi file as for the SNP6 arrays?

Also, can you please explain to me what python does? If I understand correctly, in the first part, it selects only some columns from the .csv file, in the second part it joins the two files and deletes the raws that have not been found. Is this correct?

 

Do you know whether any user encountered the same problem and how did they solve it?

Sorry for all these questions but I am not a bioinformatitian so to me it is quite difficult to approach this issue!

 

Thanking you in adavance,

 

Best,

 

Monica

[Monica Messina]

Dear Cheng,

 

we were finally able to generate an annotation file suitable for dChip so that now I can visualize the Inferred log2 ratio image and curate the CNA. However, I still have some problem with the genotyping files gerated by CHAS that have the .cych extension: are they recognized by dChip?

 

Any additional information will be greatly appreciated!

 

Thanks,

 

Monica

[Dee Cronin Fenton]

Dear Cheng,

I am using dChip for microRNA analyses.  I have loaded R but the link on the dChip webpage for the R-COM package is not working (please see https://sites.google.com/site/dchipsoft/introduction-to-dchip/interface-with-the-r-software and the "R-COM binary files" link).  Please could you direct me to another way to load R-COM?  I cannot run LDA analyses in dChip.

Many thanks for your help. 

Sincerely,

Deirdre Cronin Fenton.

On Thu, Oct 17, 2013 at 1:26 PM, Monica Messina <monica....@gmail.com> wrote:

Dear Cheng,

 

we were finally able to generate an annotation file suitable for dChip so that now I can visualize the Inferred log2 ratio image and curate the CNA. However, I still have some problem with the genotyping files gerated by CHAS that have the .cych extension: are they recognized by dChip?

 

Any additional information will be greatly appreciated!

 

Thanks,

 

Monica

 

On Tuesday, November 27, 2012 6:38:21 PM UTC+1, Cheng Li wrote:

Monica,

Can you try a quick solution: copy and paste columns from Affy CSV files to resemble a dchip genome info file (save in tab-delimited text format):
https://sites.google.com/site/dchipsoft/snp-array-analysis/view-data-along-chromosome/genome-information-file

Cheng
www.ChengLiLab.org

On Tue, Nov 27, 2012 at 5:16 AM, Monica Messina <monica....@gmail.com> wrote:

Dear Cheng,

 

I am experiencing some problem in generating the genome info for cytoscan arrays. Can you provide the script to generate it by Python or the file itself?

 

Thank you for your help,

 

Monica

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