MODZ calculation in R?

[ge2sasag]

Hi,

I'm not sure if I should ask this question here, but I wonder if there is any way to calculate MODZ for a certain expression matrix (i.e., from microarray or RNA-seq) if you already have expression values calculated as robust z-score. I've been trying to do spearman pairwise correlations with cor() but I'm not sure if there's any similar code to the one available in matlab.

I want to do this because I have some expression signatures that I want to correlate with L1000 profiles in cMAP database (i.e., to do PCA) and I guess I should have my expression data calculated as MODZ prior comparison.

Thank you very much in advance.

Best
Gema

[tnat1031]

Hi Gema, The modz algorithm is not currently available in cmapR but it's something we've been meaning to add. This is a great reason to do it! Please look for an update to the repository in the next couple of days. Thanks a lot, Ted

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On Wed, Feb 21, 2018 at 11:48 AM ge2sasag ***@***.***> wrote: Hi, I'm not sure if I should ask this question here, but I wonder if there is any way to calculate MODZ for a certain expression matrix (i.e., from microarray or RNA-seq) if you already have expression values calculated as robust z-score. I've been trying to do spearman pairwise correlations with cor() but I'm not sure if there's any similar code to the one available in matlab. I want to do this because I have some expression signatures that I want to correlate with L1000 profiles in cMAP database (i.e., to do PCA) and I guess I should have my expression data calculated as MODZ prior comparison. Thank you very much in advance. Best Gema — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB3i7ycow6j3NHoZZRODHU5C2gQNkgSyks5tXEjhgaJpZM4SN97n> .

[ge2sasag]

Hi Ted,

Thanks a lot! that would be really helpful!
I look forward the update

Best
Gema

[ge2sasag]

Hi Ted!

How is it going with the update? :)

Best
Gema

[ge2sasag]

Hi,

Any chance to have MODZ calculation in R soon? Thank you very much in advance

Best
Gema

[tnat1031]

Hi Gema,

I'm very sorry for the delay on this. We have just added the modz calculation to cmapR in the function distil. Please have a look and let me know if you have any questions.

Best,
Ted