mapExpressionToReactions returning NaN array

[anilk991]

The [expressionRxns, parsedGPR, gene_used] = mapExpressionToReactions(model, expData); is giving expressionRxns variable as entirely NaN values. But parsedGPR and gene_used return cell array. The genes in expData are in entrez format without version, on the other hand genes in model.genes are in entrez format with version.

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[rmtfleming]

expressionRxns(j) = NaN when there is no expression data for the corresponding gene.

On Wed, 23 Feb 2022 at 11:33, anilk991 @.***> wrote:

The [expressionRxns, parsedGPR, gene_used] = mapExpressionToReactions(model, expData); is giving expressionRxns variable as entirely NaN values. But parsedGPR and gene_used return cell array. The genes in expData are in entrez format without version, on the other hand genes in model.genes are in entrez format with version.

I hereby confirm that I have:

• [ X] Tried to solve the issue on my own
• [ X] Retried to run my code with the latest version of The COBRA Toolbox
• [ X] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

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[anilk991]

The issue is that all the reactions are coming out as NaN.

On Wed, Feb 23, 2022, 18:49 Ronan M.T. Fleming @.***> wrote:

expressionRxns(j) = NaN when there is no expression data for the corresponding gene.

On Wed, 23 Feb 2022 at 11:33, anilk991 @.***> wrote:

The [expressionRxns, parsedGPR, gene_used] = mapExpressionToReactions(model, expData); is giving expressionRxns variable as entirely NaN values. But parsedGPR and gene_used return cell array. The genes in expData are in entrez format without version, on the other hand genes in model.genes are in entrez format with version.

I hereby confirm that I have:

• [ X] Tried to solve the issue on my own
• [ X] Retried to run my code with the latest version of The COBRA Toolbox
• [ X] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1942, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAQMEOVCAGBVNRMG2ZUO3UDU4TAXTANCNFSM5PECQ55Q

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

---

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

---

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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[rmtfleming]

what is the input? are you sure those genes correspond to the reactions?

On Wed, 23 Feb 2022 at 13:34, anilk991 @.***> wrote:

The issue is that all the reactions are coming out as NaN.

On Wed, Feb 23, 2022, 18:49 Ronan M.T. Fleming @.***> wrote:

expressionRxns(j) = NaN when there is no expression data for the corresponding gene.

On Wed, 23 Feb 2022 at 11:33, anilk991 @.***> wrote:

The [expressionRxns, parsedGPR, gene_used] = mapExpressionToReactions(model, expData); is giving expressionRxns variable as entirely NaN values. But parsedGPR and gene_used return cell array. The genes in expData are in entrez format without version, on the other hand genes in model.genes are in entrez format with version.

I hereby confirm that I have:

• [ X] Tried to solve the issue on my own
• [ X] Retried to run my code with the latest version of The COBRA Toolbox
• [ X] Checked that a similar issue has not already been opened

(Note: You may replace [ ] with [X] to check the box)

— Reply to this email directly, view it on GitHub https://github.com/opencobra/cobratoolbox/issues/1942, or unsubscribe <

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.

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

---

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

---

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.

Associate Professor, School of Medicine, National University of Ireland, Galway. & Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu

Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming

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[anilk991]

expData is in form of a struct with expData.gene as double array with entrez gene ids and expData.value as logical array.