Regd DiSCoVER

[ravi]

Hi,

When using DiSCoVER module;

1 - Is it okay to use TPM or RPKM values as gene expression values?

2 - Can this algorithm be used for samples from different treatment groups in one .csv data sheet? For instance can I include tumour subtypes in one .csv sheet or is it ideal to prepare separate .csv sheets for each subtype/group of samples ?

Your expert suggestion will help.

Thank you,

Ravi.

[Michael Reich]

Hi Ravi,

1. You should use TPM values for input to DiSCoVER. 

2. DiSCoVER is designed to run on one treatment/control pair at a time, so there should not be different treatment groups in the treatment .csv file.

Please let me know if I can answer any other questions.

Best,
Michael

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Michael Reich
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University of California, San Diego
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[ravi velaga]

Hi Michael,

Thank you for the information and reply.

Is it also compatible to use normalised total read counts after DESeq2 normalisation?

Your suggestion will help.

Thank you,

Ravi.

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[Michael Reich]

Hi Ravi,

Yes, you can use normalized DESeq2 read counts.

Best,
Michael

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[ravi velaga]

Thank you, Michael.

Best regards,

Ravi.

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