Excution of The function "FindPattern" and "FindPattern_Multi" fail

tujchl commented 1 year ago

Hi, I followed the tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mbrain_10X.html) using my own data. The following is my code:

count1 = GetAssayData(J001.A,slot="counts") count2 = GetAssayData(J002.A,slot="counts") location1 = GetTissueCoordinates(J001.A) location2 = GetTissueCoordinates(J002.A) spa1 = SpaGene(count1, location1) spa2 = SpaGene(count2, location2) pattern1 = FindPattern(spa1) pattern1 = FindPattern(spa2) pattern = FindPattern_Multi(list(spa1,spa2), nPattern = 25) Everything works fine until excuting FindPattern and FindPattern_Multi. Belowing is my err message: Error in Rcpp_nmf_dense(data, mask_matrix, tol, maxit, getOption("RcppML.verbose"), : Expecting a single value: [extent=0].

My data is 10X Visium data. Data preprocessing basically followed the spatial vignette from Seurat (https://satijalab.org/seurat/articles/spatial_vignette.html). Everything works fine and no err ocuurs.

liuqivandy commented 1 year ago

Didn’t see anything wrong with the code. Do you mind share one of your data? Thanks Qi

From: tujchl @.> Date: Saturday, August 27, 2022 at 1:48 AM To: liuqivandy/SpaGene @.> Cc: Subscribed @.> Subject: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Hi, I followed the tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mbrain_10X.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmbrain_10X.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022485647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2F8c4rxCre%2FGuESgSmApG8R0EgcETJB%2BARl4IsNrM9s%3D&reserved=0) using my own data. The following is my code:

count1 = GetAssayData(J001.A,slot="counts") count2 = GetAssayData(J002.A,slot="counts") location1 = GetTissueCoordinates(J001.A) location2 = GetTissueCoordinates(J002.A) spa1 = SpaGene(count1, location1) spa2 = SpaGene(count2, location2) pattern1 = FindPattern(spa1) pattern1 = FindPattern(spa2) pattern = FindPattern_Multi(list(spa1,spa2), nPattern = 25) Everything works fine until excuting FindPattern and FindPattern_Multi. Belowing is my err message: Error in Rcpp_nmf_dense(data, mask_matrix, tol, maxit, getOption("RcppML.verbose"), : Expecting a single value: [extent=0].

My data is 10X Visium data. Data preprocessing basically followed the spatial vignette from Seurat (https://satijalab.org/seurat/articles/spatial_vignette.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fspatial_vignette.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022641883%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CojZCqhMQ%2FLlgq%2BZl%2BNFKtkLajqM977GVC8NBx%2FTLDo%3D&reserved=0). Everything works fine and no err ocuurs.

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tujchl commented 1 year ago

Didn’t see anything wrong with the code. Do you mind share one of your data? Thanks Qi From: tujchl @.> Date: Saturday, August 27, 2022 at 1:48 AM To: liuqivandy/SpaGene @.> Cc: Subscribed @.> Subject: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification Hi, I followed the tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mbrain_10X.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmbrain_10X.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022485647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2F8c4rxCre%2FGuESgSmApG8R0EgcETJB%2BARl4IsNrM9s%3D&reserved=0) using my own data. The following is my code: count1 = GetAssayData(J001.A,slot="counts") count2 = GetAssayData(J002.A,slot="counts") location1 = GetTissueCoordinates(J001.A) location2 = GetTissueCoordinates(J002.A) spa1 = SpaGene(count1, location1) spa2 = SpaGene(count2, location2) pattern1 = FindPattern(spa1) pattern1 = FindPattern(spa2) pattern = FindPattern_Multi(list(spa1,spa2), nPattern = 25) Everything works fine until excuting FindPattern and FindPattern_Multi. Belowing is my err message: Error in Rcpp_nmf_dense(data, mask_matrix, tol, maxit, getOption("RcppML.verbose"), : Expecting a single value: [extent=0]. My data is 10X Visium data. Data preprocessing basically followed the spatial vignette from Seurat (https://satijalab.org/seurat/articles/spatial_vignette.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fspatial_vignette.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022641883%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CojZCqhMQ%2FLlgq%2BZl%2BNFKtkLajqM977GVC8NBx%2FTLDo%3D&reserved=0). Everything works fine and no err ocuurs. — Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fissues%2F1&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022641883%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=y3pavke4xDIqZu6GnResG5L9hhsjz4LgHQDEBR0%2B27U%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAIH2RCJXDKNJXAJCVBZTAJLV3G23HANCNFSM57Y2SLAA&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022641883%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=61K4RZgxoBZ%2BElYyBdXZKb5Vm8qJLzXBkyd5u8AXy1o%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

Thanks, Dr. qi, I`d like to share one of my dataset with you to fix the err. Belowing is the link to download the data.

https://pan.baidu.com/s/1-sr1SDqNwOrl1p_fm_vzIA?pwd=c6n9

Hope it will be helpful

liuqivandy commented 1 year ago

Unfortunately, I cannot download the data. Any other way to share the data?

From: tujchl @.> Date: Saturday, August 27, 2022 at 10:03 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Thanks, Dr. qi, I`d like to share one of my dataset with you to fix the err. Belowing is the link to download the data.

https://pan.baidu.com/s/1-sr1SDqNwOrl1p_fm_vzIA?pwd=c6n9 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpan.baidu.com%2Fs%2F1-sr1SDqNwOrl1p_fm_vzIA%3Fpwd%3Dc6n9&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OypUjmmwEVQ%2BLIV0RRTJnQq2I%2Bqohs3W%2B6%2Bid%2Bhd46w%3D&reserved=0

Hope it will be helpful

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tujchl commented 1 year ago

Unfortunately, I cannot download the data. Any other way to share the data? From: tujchl @.> Date: Saturday, August 27, 2022 at 10:03 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification Didn’t see anything wrong with the code. Do you mind share one of your data? Thanks Qi From: tujchl @.> Date: Saturday, August 27, 2022 at 1:48 AM To: liuqivandy/SpaGene @.> Cc: Subscribed @.> Subject: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fissues%2F1&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FOMQts7e6vaxKhuuSdK4CgPgk2ki%2FXV%2B2VlqgMgyWRY%3D&reserved=0) You don't often get email from @. Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification Hi, I followed the tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mbrain_10X.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmbrain_10X.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3OT0VLiF%2FatEMpvQnysFIPqjbTvKEbv6T5Q0hlk3ZGU%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmbrain_10X.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022485647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2F8c4rxCre%2FGuESgSmApG8R0EgcETJB%2BARl4IsNrM9s%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmbrain_10X.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3OT0VLiF%2FatEMpvQnysFIPqjbTvKEbv6T5Q0hlk3ZGU%3D&reserved=0) using my own data. The following is my code: count1 = GetAssayData(J001.A,slot="counts") count2 = GetAssayData(J002.A,slot="counts") location1 = GetTissueCoordinates(J001.A) location2 = GetTissueCoordinates(J002.A) spa1 = SpaGene(count1, location1) spa2 = SpaGene(count2, location2) pattern1 = FindPattern(spa1) pattern1 = FindPattern(spa2) pattern = FindPattern_Multi(list(spa1,spa2), nPattern = 25) Everything works fine until excuting FindPattern and FindPattern_Multi. Belowing is my err message: Error in Rcpp_nmf_dense(data, mask_matrix, tol, maxit, getOption("RcppML.verbose"), : Expecting a single value: [extent=0]. My data is 10X Visium data. Data preprocessing basically followed the spatial vignette from Seurat (https://satijalab.org/seurat/articles/spatial_vignette.html https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fspatial_vignette.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T%2FDBxmCPgDBxuoSpRGHQE5B82m4Msh1x8coMb%2FYrJ%2Fw%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fspatial_vignette.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C9e681b49e7f742317f0808da87f820f0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637971797022641883%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CojZCqhMQ%2FLlgq%2BZl%2BNFKtkLajqM977GVC8NBx%2FTLDo%3D&reserved=0 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsatijalab.org%2Fseurat%2Farticles%2Fspatial_vignette.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=T%2FDBxmCPgDBxuoSpRGHQE5B82m4Msh1x8coMb%2FYrJ%2Fw%3D&reserved=0). 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You are receiving this because you are subscribed to this thread.Message ID: @.> Thanks, Dr. qi, I`d like to share one of my dataset with you to fix the err. Belowing is the link to download the data. https://pan.baidu.com/s/1-sr1SDqNwOrl1p_fm_vzIA?pwd=c6n9 https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpan.baidu.com%2Fs%2F1-sr1SDqNwOrl1p_fm_vzIA%3Fpwd%3Dc6n9&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OypUjmmwEVQ%2BLIV0RRTJnQq2I%2Bqohs3W%2B6%2Bid%2Bhd46w%3D&reserved=0 Hope it will be helpful — Reply to this email directly, view it on GitHubhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fissues%2F1%23issuecomment-1229363326&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986603835%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OiUMpgMJCktt%2BJr4Kq8jx934fmmSUy%2FPhkcwi0UXUeo%3D&reserved=0, or unsubscribehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAIH2RCMRS27VB3QUAWR43F3V3LJHHANCNFSM57Y2SLAA&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C731e793aaebc4757476808da88a1da10%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637972525986760065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xqvyaWxVbrVmAipuXEpu1nhOGr4%2Bj%2F4CKJ%2FlwT2Ql%2Fs%3D&reserved=0. 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Do you have E-mail which could receieve mail with large size attachment (~240M)? I can send it to you via mail.

liuqivandy commented 1 year ago

My email cannot receive such large file. Would you please take a look at spa1 (the result from SpaGene) ? I basically use RcppML (another R package) on spa1 to find NMF.

From: tujchl @.> Date: Saturday, August 27, 2022 at 10:36 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Do you have E-mail which could receieve mail with large size attachment (~240M)? I can send it to you via mail.

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tujchl commented 1 year ago

Belowing is the information related to spa1 via str(spa1):

List of 2 $ normexp :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. ..@ i : int [1:19082694] 6 9 13 18 25 26 31 35 39 45 ... .. ..@ p : int [1:3056] 0 5201 12202 18802 25784 32754 39770 46718 53784 60608 ... .. ..@ Dim : int [1:2] 15563 3055 .. ..@ Dimnames:List of 2 .. .. ..$ : chr [1:15563] "SAMD11" "NOC2L" "KLHL17" "PLEKHN1" ... .. .. ..$ : chr [1:3055] "AAACAGAGCGACTCCT-1" "AAACAGCTTTCAGAAG-1" "AAACAGGGTCTATATT-1" "AAACCGGGTAGGTACC-1" ... .. ..@ x : num [1:19082694] 0.462 0.462 1.837 0.776 1.015 ... .. ..@ factors : list() $ spagene_res:'data.frame': 15563 obs. of 4 variables: ..$ score: num [1:15563] 14.3 14.4 14.6 14.5 14.5 ... ..$ zval : num [1:15563] -5.837 -3.334 -0.252 -2.785 -1.076 ... ..$ pval : num [1:15563] 2.66e-09 4.27e-04 4.01e-01 2.68e-03 1.41e-01 ... ..$ adjp : num [1:15563] 9.33e-09 8.29e-04 4.65e-01 4.62e-03 1.84e-01 ...

BTW: I found the size of spa1 is relative small (~40MB). Can I send it to you if it is helpful?

liuqivandy commented 1 year ago

Can you find another way to share the data?

From: tujchl @.> Date: Monday, August 29, 2022 at 12:17 AM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1) You don't often get email from @.*** Learn why this is importanthttps://aka.ms/LearnAboutSenderIdentification

Belowing is the information related to spa1 via str(spa1):

List of 2 $ normexp :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots .. ..@ i : int [1:19082694] 6 9 13 18 25 26 31 35 39 45 ... .. ..@ p : int [1:3056] 0 5201 12202 18802 25784 32754 39770 46718 53784 60608 ... .. ..@ Dim : int [1:2] 15563 3055 .. ..@ Dimnames:List of 2 .. .. ..$ : chr [1:15563] "SAMD11" "NOC2L" "KLHL17" "PLEKHN1" ... .. .. ..$ : chr [1:3055] "AAACAGAGCGACTCCT-1" "AAACAGCTTTCAGAAG-1" "AAACAGGGTCTATATT-1" "AAACCGGGTAGGTACC-1" ... .. ..@ x : num [1:19082694] 0.462 0.462 1.837 0.776 1.015 ... .. ..@ factors : list() $ spagene_res:'data.frame': 15563 obs. of 4 variables: ..$ score: num [1:15563] 14.3 14.4 14.6 14.5 14.5 ... ..$ zval : num [1:15563] -5.837 -3.334 -0.252 -2.785 -1.076 ... ..$ pval : num [1:15563] 2.66e-09 4.27e-04 4.01e-01 2.68e-03 1.41e-01 ... ..$ adjp : num [1:15563] 9.33e-09 8.29e-04 4.65e-01 4.62e-03 1.84e-01 ...

BTW: I found the size of spa1 is relative small (~40MB). Can I send it to you if it is helpful?

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tujchl commented 1 year ago

After several rounds of trying, I finally uploaded my dataset onto the dropbox. Belowing is the sharing link:

https://www.dropbox.com/s/088zobzuuaqnh3q/J001.A.Rdata?dl=0

Hope it could be helpful

liuqivandy commented 1 year ago

Great. I run the data successfully without any problem. Please find the pattern and genes associated with the pattern attached. I think the problem is due to RcppML package installed in your computing environment.

From: tujchl @.> Date: Friday, September 2, 2022 at 9:07 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1)

After several rounds of trying, I finally uploaded my dataset onto the dropbox. Belowing is the sharing link:

SpaGenehttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dropbox.com%2Fs%2F088zobzuuaqnh3q%2FJ001.A.Rdata%3Fdl%3D0&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7Ce3571bc58c064a6ac40608da8d51154e%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637977676649879538%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1ZHEdqfwlKyUn1TvXMKcewQUH5hX30vKupSEB1pg3zc%3D&reserved=0

Hope it could be helpful

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liuqivandy commented 1 year ago

Great. I run the data successfully without any problem. Please find the pattern and genes associated with the pattern attached. I think the problem is due to RcppML package installed in your computing environment. Screen Shot 2022-09-02 at 10 08 47 PM

tujchl commented 1 year ago

Thanks, The version of RcppML installed on my machine is "v0.5.4". The version of R is 4.1.0 (2021-05-18). Can I re-install the RcppML package to solve this promble? What is the version of RcppML on your machine?

tujchl commented 1 year ago

Well, re-installation of RcppML could indeed solve this err. However, we should re-install the RcppML by "install.packages('RcppML')" other than "devtools::install_github("zdebruine/RcppML")" which may install a dev-version and cause the err.

liuqivandy commented 1 year ago

Great. Thanks for letting me know.

From: tujchl @.> Date: Saturday, September 3, 2022 at 3:28 AM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] Excution of The function "FindPattern" and "FindPattern_Multi" fail (Issue #1)

Well, re-installation of RcppML could indeed solve this err. However, we should re-install the RcppML by "install.packages('RcppML')" other than "devtools::install_github("zdebruine/RcppML")" which may install a dev-version and cause the err.

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liuqivandy / SpaGene

Excution of The function "FindPattern" and "FindPattern_Multi" fail #1