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yunzhang813 / FUNNEL-GSEA-R-Package

Zhang et al. 2017. FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. Bioinformatics, 33(13), 1944-1952.
https://doi.org/10.1093/bioinformatics/btx104
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Error in interpp.old missing values and Infs not allowed #2

Open qvhaelen opened 5 years ago

qvhaelen commented 5 years ago

Hello,

I try to use your method FUNNEL with a time series data (8 time points) and pathway database. I tried with the main function result <- FUNNEL.GSEA(X, tt, genesets), this example works well and works also when replacing genesets by my own pathway list "pathway_gene_list": FUNNEL.GSEA(X, tt, pathway_gene_list). however, when using my own transcription data, I got an error:

Error in interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate, : missing values and Infs not allowed

the vector tt is adapted to contain the right number of time points. I have checked if the format of my matrix is the same than the one provided as an example and it is same data type:

str(X) num [1:11189, 1:16] 2.26 9.38 1.96 8.19 7.53 ...

str(x3array) num [1:20340, 1:8] 0.366 0 1.077 0.169 0.139 ...

there is no NA in the file. I do not know what to do or where to look to fix this error. Any advise or suggestion will be helpful?

thank you

Quentin

yunzhang813 commented 5 years ago

Hi Quentin,

Thank you for bringing this issue to us. This error message is because interpp.old() is deprecated in a package called ‘akima’ that FUNNEL depends on. Please see the link below. https://www.rdocumentation.org/packages/akima/versions/0.6-2/topics/interpp.old

For a quick fix, you may look for an old version of akima, or locate the interpp.old() function and replace it with interpp() as noted in the above page.

Your message has brought me series attention on this. However, I am not able to work on this in coming weekends. If you can wait, I plan to submit an updated version in a month or so.

Please let us know if you have any other feedbacks for the package.

Thanks a lot, Yun

From: qvhaelen notifications@github.com Reply-To: yunzhang813/FUNNEL-GSEA-R-Package reply@reply.github.com Date: Friday, September 21, 2018 at 5:25 AM To: yunzhang813/FUNNEL-GSEA-R-Package FUNNEL-GSEA-R-Package@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [yunzhang813/FUNNEL-GSEA-R-Package] Error in interpp.old missing values and Infs not allowed (#2)

Hello,

I try to use your method FUNNEL with a time series data (8 time points) and pathway database. I tried with the main function result <- FUNNEL.GSEA(X, tt, genesets), this example works well and works also when replacing genesets by my own pathway list "pathway_gene_list": FUNNEL.GSEA(X, tt, pathway_gene_list). however, when using my own transcription data, I got an error:

Error in interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate, : missing values and Infs not allowed

the vector tt is adapted to contain the right number of time points. I have checked if the format of my matrix is the same than the one provided as an example and it is same data type:

str(X) num [1:11189, 1:16] 2.26 9.38 1.96 8.19 7.53 ...

str(x3array) num [1:20340, 1:8] 0.366 0 1.077 0.169 0.139 ...

there is no NA in the file. I do not know what to do or where to look to fix this error. Any advise or suggestion will be helpful?

thank you

Quentin

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qvhaelen commented 5 years ago

hello

Thank you for the answer and information provided. nevertheless, I have to say I am still confused because of the following. When running FUNNEL using the example provided in the package, result <- FUNNEL.GSEA(X, tt, genesets), the program does indicate a warning saying that Warning messages: 1: In interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate, : interpp.old() is deprecated, future versions will only provide interpp()

But it is working anyway. The error message which stops the calculation (Error in interpp.old(x, y, z, xo, yo, ncp = 0, extrap = FALSE, duplicate = duplicate, : missing values and Infs not allowed) appears only when running the same function using my own data X rather than the one provided in the FUNNEL package. Modifying the lsit of pathways for example does not generate error message.

thank you

quentin