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Error with CNV.import in conumee2.0 for EPICv2 #1

Open biopyju opened 1 year ago

biopyju commented 1 year ago

Hi,

First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:

CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")

Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature ‘"character", "character", "character"’

I would be grateful for your help.

Best regards.

bjarnedae commented 1 year ago

Hi,

thank you for your interest in the conumee update! Since we are currently in the process of updating the vignette (that is not online yet), I send you some instructions to use conumee with the EPICv2 array here:

Please use the new CNV.import function to import your idat files:

CNV.import(array_type = “EPICv2”, directory = “”, sample_sheet = “”)

The sample sheet should have at least three columns including the Sample_Name, the Sentrix_ID and the Sentrix_Position (these column names are case sensitive what might be the reason for the error message that you obtained). Please use the resulting dataframe as input for the CNV.load function subsequently.

Additionally, please specify the correct array type in the CNV.fit() function: CNV.fit(array_type = “EPICv2”)

Please do not hesitate to contact me in case you run into any problems/difficulties with the update.

Best wishes, Bjarne

Bjarne Dänekas Graduate Student, Hovestadt Lab Department of Pediatric Oncology

Dana Farber Cancer Institute Harvard Medical School 450 Brookline Avenue Boston, MA 02215-5450

[PastedGraphic-2.png]

Am 26.07.2023 um 12:42 schrieb biopyju @.***>:

    External Email - Use Caution

Hi,

First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:

CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")

Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature ‘"character", "character", "character"’

I would be grateful for your help.

Best regards.

— Reply to this email directly, view it on GitHubhttps://secure-web.cisco.com/1uFHYUv3_8eangPgl71ICETq1Xa-9tECZOX3oBe-P5QHjk91QkYMNFgixuPHWxNAyVCGUHT7ZvShPsjwpbz3pHCpKkceFqmvRgGbl2EehhOSvVm0nGJOjsJKeRvg8l2bgaw-t7mmGZghtLCY2Rk0MtbZ0WblcawhdjkcZTJ7tzxcpaUucRZUrUvPlgcXWrtr07eut3laMZ7Rub5-Fve0lMc_lwUMCoCdXstmV-kwQhXH3WertD28RmHBZro4KMPMbajQklN_KGoL9z5TA492QXkNUFR50OeCvqhxkuD9fNFCBFu9bmqix3e_nOMHko6mgQV5UDfjb2hw0YZqp_XdPpQ/https%3A%2F%2Fgithub.com%2Fbjarnedae%2Fconumee-2%2Fissues%2F1, or unsubscribehttps://secure-web.cisco.com/1aqAQaQ10k7uOkeIRcP_y1AbEdokF6dRDEFaPPeo2V-n5y9RHRUN3cSdfCxtL-OOFF_b0wNJrsjAIRM3xJp52bvn6YrrRyqVSae4GwSaGL23Y2gXkSNRNU9vIZl94nmzXedemVMI115jx-9T8rzNmRTCr-lRxvugzkuBU3MYOGi8glflDWYfqYbdJygy5n3Hma1kW63eoyTId68Ha0X5m_YSDxj3-Eu2pU6LZTAC4_PDQF3GrNQwGvXNF4sGmaEVG1IXKxEfKsxLBLD4CHs0GW0Is82r8Q5gBLYvl1EwXzCI7Syt1XsDJAL91gGoVQTNcDwS5UZPWdq8sm_AN0Sv01Q/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAZJ7TFQFLKQXHKMWZSYAWXDXSDYA3ANCNFSM6AAAAAA2YMJ74M. You are receiving this because you are subscribed to this thread.Message ID: @.***>

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biopyju commented 1 year ago

Hi Bjarne,

Thank you for your quick response!

I gave a new try to conumee2.0 with your instructions, but I always get the same error. I checked twice all parameters. I use the original samplesheet from Illumina website with the good case for column IDs.

I join you my files, perhaps I'm missing something...

Thank you for your help! Best regards,

Julien.

Dr Julien Boyer Pathologist Nice Cancer Center France

Le sam. 29 juil. 2023 à 15:52, Bjarne Dänekas @.***> a écrit :

Hi,

thank you for your interest in the conumee update! Since we are currently in the process of updating the vignette (that is not online yet), I send you some instructions to use conumee with the EPICv2 array here:

Please use the new CNV.import function to import your idat files:

CNV.import(array_type = “EPICv2”, directory = “”, sample_sheet = “”)

The sample sheet should have at least three columns including the Sample_Name, the Sentrix_ID and the Sentrix_Position (these column names are case sensitive what might be the reason for the error message that you obtained). Please use the resulting dataframe as input for the CNV.load function subsequently.

Additionally, please specify the correct array type in the CNV.fit() function: CNV.fit(array_type = “EPICv2”)

Please do not hesitate to contact me in case you run into any problems/difficulties with the update.

Best wishes, Bjarne

Bjarne Dänekas Graduate Student, Hovestadt Lab Department of Pediatric Oncology

Dana Farber Cancer Institute Harvard Medical School 450 Brookline Avenue Boston, MA 02215-5450

[PastedGraphic-2.png]

Am 26.07.2023 um 12:42 schrieb biopyju @.***>:

External Email - Use Caution

Hi,

First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:

CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")

Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature ‘"character", "character", "character"’

I would be grateful for your help.

Best regards.

— Reply to this email directly, view it on GitHub< https://secure-web.cisco.com/1uFHYUv3_8eangPgl71ICETq1Xa-9tECZOX3oBe-P5QHjk91QkYMNFgixuPHWxNAyVCGUHT7ZvShPsjwpbz3pHCpKkceFqmvRgGbl2EehhOSvVm0nGJOjsJKeRvg8l2bgaw-t7mmGZghtLCY2Rk0MtbZ0WblcawhdjkcZTJ7tzxcpaUucRZUrUvPlgcXWrtr07eut3laMZ7Rub5-Fve0lMc_lwUMCoCdXstmV-kwQhXH3WertD28RmHBZro4KMPMbajQklN_KGoL9z5TA492QXkNUFR50OeCvqhxkuD9fNFCBFu9bmqix3e_nOMHko6mgQV5UDfjb2hw0YZqp_XdPpQ/https%3A%2F%2Fgithub.com%2Fbjarnedae%2Fconumee-2%2Fissues%2F1>, or unsubscribe< https://secure-web.cisco.com/1aqAQaQ10k7uOkeIRcP_y1AbEdokF6dRDEFaPPeo2V-n5y9RHRUN3cSdfCxtL-OOFF_b0wNJrsjAIRM3xJp52bvn6YrrRyqVSae4GwSaGL23Y2gXkSNRNU9vIZl94nmzXedemVMI115jx-9T8rzNmRTCr-lRxvugzkuBU3MYOGi8glflDWYfqYbdJygy5n3Hma1kW63eoyTId68Ha0X5m_YSDxj3-Eu2pU6LZTAC4_PDQF3GrNQwGvXNF4sGmaEVG1IXKxEfKsxLBLD4CHs0GW0Is82r8Q5gBLYvl1EwXzCI7Syt1XsDJAL91gGoVQTNcDwS5UZPWdq8sm_AN0Sv01Q/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAZJ7TFQFLKQXHKMWZSYAWXDXSDYA3ANCNFSM6AAAAAA2YMJ74M>.

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bjarnedae commented 1 year ago

Hi Julien,

I ran the analysis with the same dataset as well and did some troubleshooting. For the parameter sample_sheet within the CNV.import function, a tibble or a dataframe is required as input. The function doesn't load the samplesheet from the directory by itself. Maybe you could give it a try with this code (adapted to your local directory):

library(conumee2.0) library(readr)

sample_sheet <- read_csv("C:/Users/pereze/Downloads/Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv", skip = 7) load.data <- CNV.import(array_type = "EPICv2", directory = "C:/Users/pereze/Downloads/raw_idats", sample_sheet = sample_sheet) load.data <- CNV.load(load.data)

Thanks again for your message! This feedback is very helpful for us and we'll make sure that the vignette will clearly explain how to load the samples.

Best regards, Bjarne

From: biopyju @.> Sent: Monday, July 31, 2023 3:07 AM To: bjarnedae/conumee-2 @.> Cc: Danekas, Bjarne @.>; Comment @.> Subject: Re: [bjarnedae/conumee-2] Error with CNV.import in conumee2.0 for EPICv2 (Issue #1)

    External Email - Use Caution

Hi Bjarne,

Thank you for your quick response!

I gave a new try to conumee2.0 with your instructions, but I always get the same error. I checked twice all parameters. I use the original samplesheet from Illumina website with the good case for column IDs.

I join you my files, perhaps I'm missing something...

Thank you for your help! Best regards,

Julien.

Dr Julien Boyer Pathologist Nice Cancer Center France

Le sam. 29 juil. 2023 à 15:52, Bjarne Dänekas @.***> a écrit :

Hi,

thank you for your interest in the conumee update! Since we are currently in the process of updating the vignette (that is not online yet), I send you some instructions to use conumee with the EPICv2 array here:

Please use the new CNV.import function to import your idat files:

CNV.import(array_type = “EPICv2”, directory = “”, sample_sheet = “”)

The sample sheet should have at least three columns including the Sample_Name, the Sentrix_ID and the Sentrix_Position (these column names are case sensitive what might be the reason for the error message that you obtained). Please use the resulting dataframe as input for the CNV.load function subsequently.

Additionally, please specify the correct array type in the CNV.fit() function: CNV.fit(array_type = “EPICv2”)

Please do not hesitate to contact me in case you run into any problems/difficulties with the update.

Best wishes, Bjarne

Bjarne Dänekas Graduate Student, Hovestadt Lab Department of Pediatric Oncology

Dana Farber Cancer Institute Harvard Medical School 450 Brookline Avenue Boston, MA 02215-5450

[PastedGraphic-2.png]

Am 26.07.2023 um 12:42 schrieb biopyju @.***>:

External Email - Use Caution

Hi,

First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:

CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")

Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature ‘"character", "character", "character"’

I would be grateful for your help.

Best regards.

— Reply to this email directly, view it on GitHub< https://secure-web.cisco.com/1uFHYUv3_8eangPgl71ICETq1Xa-9tECZOX3oBe-P5QHjk91QkYMNFgixuPHWxNAyVCGUHT7ZvShPsjwpbz3pHCpKkceFqmvRgGbl2EehhOSvVm0nGJOjsJKeRvg8l2bgaw-t7mmGZghtLCY2Rk0MtbZ0WblcawhdjkcZTJ7tzxcpaUucRZUrUvPlgcXWrtr07eut3laMZ7Rub5-Fve0lMc_lwUMCoCdXstmV-kwQhXH3WertD28RmHBZro4KMPMbajQklN_KGoL9z5TA492QXkNUFR50OeCvqhxkuD9fNFCBFu9bmqix3e_nOMHko6mgQV5UDfjb2hw0YZqp_XdPpQ/https%3A%2F%2Fgithub.com%2Fbjarnedae%2Fconumee-2%2Fissues%2F1>, or unsubscribe< https://secure-web.cisco.com/1aqAQaQ10k7uOkeIRcP_y1AbEdokF6dRDEFaPPeo2V-n5y9RHRUN3cSdfCxtL-OOFF_b0wNJrsjAIRM3xJp52bvn6YrrRyqVSae4GwSaGL23Y2gXkSNRNU9vIZl94nmzXedemVMI115jx-9T8rzNmRTCr-lRxvugzkuBU3MYOGi8glflDWYfqYbdJygy5n3Hma1kW63eoyTId68Ha0X5m_YSDxj3-Eu2pU6LZTAC4_PDQF3GrNQwGvXNF4sGmaEVG1IXKxEfKsxLBLD4CHs0GW0Is82r8Q5gBLYvl1EwXzCI7Syt1XsDJAL91gGoVQTNcDwS5UZPWdq8sm_AN0Sv01Q/https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAZJ7TFQFLKQXHKMWZSYAWXDXSDYA3ANCNFSM6AAAAAA2YMJ74M>.

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biopyju commented 1 year ago

Bjarne,

Wonderful! My first annotated CNV profile with EPICv2!

Big thanks for your help! Big thanks for the work of your team!

If you need a beta tester for conumee, vignette or other, please don't hesitate, I'm here!

Have a great day, Julien.

Le lun. 31 juil. 2023 à 10:21, Bjarne Dänekas @.***> a écrit :

Hi Julien,

I ran the analysis with the same dataset as well and did some troubleshooting. For the parameter sample_sheet within the CNV.import function, a tibble or a dataframe is required as input. The function doesn't load the samplesheet from the directory by itself. Maybe you could give it a try with this code (adapted to your local directory):

library(conumee2.0) library(readr)

sample_sheet <- read_csv("C:/Users/pereze/Downloads/Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv", skip = 7) load.data <- CNV.import(array_type = "EPICv2", directory = "C:/Users/pereze/Downloads/raw_idats", sample_sheet = sample_sheet) load.data <- CNV.load(load.data)

Thanks again for your message! This feedback is very helpful for us and we'll make sure that the vignette will clearly explain how to load the samples.

Best regards, Bjarne

From: biopyju @.> Sent: Monday, July 31, 2023 3:07 AM To: bjarnedae/conumee-2 @.> Cc: Danekas, Bjarne @.>; Comment @.> Subject: Re: [bjarnedae/conumee-2] Error with CNV.import in conumee2.0 for EPICv2 (Issue #1)

External Email - Use Caution

Hi Bjarne,

Thank you for your quick response!

I gave a new try to conumee2.0 with your instructions, but I always get the same error. I checked twice all parameters. I use the original samplesheet from Illumina website with the good case for column IDs.

I join you my files, perhaps I'm missing something...

Thank you for your help! Best regards,

Julien.

Dr Julien Boyer Pathologist Nice Cancer Center France

Le sam. 29 juil. 2023 à 15:52, Bjarne Dänekas @.***> a écrit :

Hi,

thank you for your interest in the conumee update! Since we are currently in the process of updating the vignette (that is not online yet), I send you some instructions to use conumee with the EPICv2 array here:

Please use the new CNV.import function to import your idat files:

CNV.import(array_type = “EPICv2”, directory = “”, sample_sheet = “”)

The sample sheet should have at least three columns including the Sample_Name, the Sentrix_ID and the Sentrix_Position (these column names are case sensitive what might be the reason for the error message that you obtained). Please use the resulting dataframe as input for the CNV.load function subsequently.

Additionally, please specify the correct array type in the CNV.fit() function: CNV.fit(array_type = “EPICv2”)

Please do not hesitate to contact me in case you run into any problems/difficulties with the update.

Best wishes, Bjarne

Bjarne Dänekas Graduate Student, Hovestadt Lab Department of Pediatric Oncology

Dana Farber Cancer Institute Harvard Medical School 450 Brookline Avenue Boston, MA 02215-5450

[PastedGraphic-2.png]

Am 26.07.2023 um 12:42 schrieb biopyju @.***>:

External Email - Use Caution

Hi,

First thank you for this adaptation of conumee. My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:

CNV.import(array_type = "EPICv2", directory = ".", sample_sheet = "Demo_EPIC-8v2-0_A1_NextSeq550_SampleSheet_3.csv")

Error in (function (classes, fdef, mtable) : impossible de trouver une methode heritee pour la fonction CNV.import pour la signature ‘"character", "character", "character"’

I would be grateful for your help.

Best regards.

— Reply to this email directly, view it on GitHub<

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simonjuleseric2 commented 3 months ago

@bjarnedae I'm unable to specify the array type using CNV.fit: error: "argument inutilisé (array_type = "EPICv2")"

bjarnedae commented 3 months ago

Dear Simon, thanks for reaching out. The most recent version of the package with some bug fixes in on the github repository from the Hovestadt Lab: https://github.com/hovestadtlab/conumee2

It would be great if you could reinstall it from there - the error message shouldn't appear then.

Kind regards, Bjarne

simonjuleseric2 commented 3 months ago

Thank you for your quick reply. Is it also possible to preprocess the samples (ex: using preprocessIllumina) when importing EPICv2 samples using CNV.import?

bjarnedae commented 3 months ago

The preprocessIllumina function is part of the minfi package. The developer version should be compatible with the new EPICv2 chip: https://github.com/hansenlab/minfi

We are currently also working on compatibility with the SeSAMe package which provides extensive preprocessing functionality as well. The update for our package will be released very soon.

simonjuleseric2 commented 3 months ago

But once the data are imported using CNV.import (for EPICv2) they are available in the dataframe format which doesn't allow for preprocessing

Additionally the link you shared still has the same issues (not accepting array_type = "EPICv2") from what I see in the github code it only accepts the following arguments: function(query, ref, anno, intercept = TRUE)

Is there any newer link?

bjarnedae commented 2 months ago

Hi, you're right - the preprocessing with minfi can't be done after CNV.import(). As it seems, minfi is still not compatible with the EPICv2 arrays. That's why we're working on combining conumee with SeSAMe. The release and a tutorial will be posted within the next weeks. For now, CNV.import() does not provide preprocessing.

For analyzing EPICv2 arrays, it's sufficient to specify the array type when creating the annotation object. Please run:

data("exclude_regions")
anno <- CNV.create_anno(array_type = "EPICv2", exclude_regions = exclude_regions)

After importing the IDATS with CNV.import() and the subsequent CNV.load(), you can run CNV.fit() without setting an array_type parameter.

Best wishes, Bjarne

simonjuleseric2 commented 2 months ago

Dear Bjarne, Thank you for your answer. Do you know when the tutorial will be available exactly? From what I understand the controls samples must be preprocessed, wouldn't that be a problem if they are and the samples analyzed aren't? (which is what is happening in the current recommended way of using the library).

Best regards, Simon

bjarnedae commented 2 months ago

Hi Simon, ideally, query and control samples should indeed be preprocessed in the same way. Since minfi is not supporting the EPICv2 arrays, we are in the process of integrating SeSAMe. The update plus tutorial will be available next week.

Best regards, Bjarne

simonjuleseric2 commented 2 months ago

Ok, thank you very much for this information. Looking forward to read next week then