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ozolotareva / DESMOND

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Data for using #3

Open LiJing-source-coder opened 2 years ago

LiJing-source-coder commented 2 years ago

If the rownames of my expression matrix occur repeated ones, then can DESMOND use for it? Thanks!

ozolotareva commented 2 years ago

Hi LiJing-source-coder,

DESMOND expects that all genes have unique names matched with network node names. I recommend dropping or renaming duplicated gene names (if you have few due to id mapping issues), aggregating expressions from the same genes (if you have many e.g. because you mapped transcripts to genes).

Btw, why do you have repeated row names in your expression matrix? Are you sure that id mapping worked correctly?

LiJing-source-coder commented 2 years ago

@.***

The initial probe ID of my expression data is the type of “AFFYMETRIX_3PRIME_IVT_ID”, but for the network data, the id of genes is usually not the type of the above. When transformed by the tool “DAVID”, I found the number of repeated ones is more than 3000. So I have the question. As you said, should I aggregate expressions from the same genes？

发件人: @.> 发送时间: 2022年3月21日 20:07 收件人: @.> 抄送: @.>; @.> 主题: Re: [ozolotareva/DESMOND] Data for using (Issue #3) 重要性: 高

Hi LiJing-source-coder,

DESMOND expects that all genes have unique names matched with network node names. I recommend dropping or renaming duplicated gene names (if you have few due to id mapping issues), aggregating expressions from the same genes (if you have many e.g. because you mapped transcripts to genes).

Btw, why do you have repeated row names in your expression matrix? Are you sure that id mapping worked correctly?

― Reply to this email directly, view it on GitHubhttps://github.com/ozolotareva/DESMOND/issues/3#issuecomment-1073814832, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYKOMKJD4DINDE5JTOIJV63VBBQ7NANCNFSM5RHOEHSQ. You are receiving this because you authored the thread.Message ID: @.***>

ozolotareva commented 2 years ago

It seems that you have Affymetrix probe ids in your expression matrix. Yes, I would aggregate probe-level intensities to gene-level simply by averaging.

You can check how we did it in our MOLI paper for example: https://github.com/hosseinshn/MOLI/blob/master/preprocessing_scr/microarrays.ipynb WGCNA::collapseRows(exprs_rma, rowGroup = anno[,geneID],rowID = anno[,"PROBEID"],method="Average")

LiJing-source-coder commented 2 years ago

Hi, ozolotareva! @.***

A error occur as above when I run DESMOND with my data. Is this because of my network data not having ‘connected component subgraphs’? Look forward to your reply. Thanks!

发件人: @.> 发送时间: 2022年3月21日 21:44 收件人: @.> 抄送: @.>; @.> 主题: Re: [ozolotareva/DESMOND] Data for using (Issue #3) 重要性: 高

It seems that you have Affymetrix probe ids in your expression matrix. Yes, I would aggregate probe-level intensities to gene-level simply by averaging.

You can check how we did it in our MOLI paper for example: https://github.com/hosseinshn/MOLI/blob/master/preprocessing_scr/microarrays.ipynb WGCNA::collapseRows(exprs_rma, rowGroup = anno[,geneID],rowID = anno[,"PROBEID"],method="Average")

― Reply to this email directly, view it on GitHubhttps://github.com/ozolotareva/DESMOND/issues/3#issuecomment-1073914533, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYKOMKOXXFXPNAMEFVUP5YTVBB4J5ANCNFSM5RHOEHSQ. You are receiving this because you authored the thread.Message ID: @.***>

ozolotareva commented 2 years ago

Hi LiJing-source-coder,

Could you please post the error message you see here?

If you share the data with me, I will try reproducing this error and either fix DESMOND or let you know how to modify inputs.

Best regards, Olga

LiJing-source-coder commented 2 years ago

Hi, ozolotareva! @.***

The error message is shown as the above picture. And the one group of input data can be found in the attachment.

Look forward to your reply, Thanks!

发件人: @.> 发送时间: 2022年3月23日 0:23 收件人: @.> 抄送: @.>; @.> 主题: Re: [ozolotareva/DESMOND] Data for using (Issue #3) 重要性: 高

Hi LiJing-source-coder,

Could you please post the error message you see here?

If you share the data with me, I will try reproducing this error and either fix DESMOND or let you know how to modify inputs.

Best regards, Olga

― Reply to this email directly, view it on GitHubhttps://github.com/ozolotareva/DESMOND/issues/3#issuecomment-1075357035, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYKOMKMQXVN4DO67W7IE6CTVBHXYBANCNFSM5RHOEHSQ. You are receiving this because you authored the thread.Message ID: @.***>

ozolotareva commented 2 years ago

Hi LiJing-source-coder,

I do not see any picture in this thread. Please double-check if it is correctly inserted/attached.

LiJing-source-coder commented 2 years ago

Hi, Olga! @.*** Sorry for this accident. I reinsert the picture here and also attach it in case. Look forward to your reply, thanks!

Best wishes,

Jing

发件人: @.> 发送时间: 2022年3月24日 22:19 收件人: @.> 抄送: @.>; @.> 主题: Re: [ozolotareva/DESMOND] Data for using (Issue #3) 重要性: 高

Hi LiJing-source-coder,

I do not see any picture in this thread. Please double-check if it is correctly inserted/attached.

― Reply to this email directly, view it on GitHubhttps://github.com/ozolotareva/DESMOND/issues/3#issuecomment-1077679587, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AYKOMKPI4TIZUP2RYLLK343VBR2V3ANCNFSM5RHOEHSQ. You are receiving this because you authored the thread.Message ID: @.***>