aroma.affymetrix

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2/23/21

Question: snp list from Affymetirx microarray files

Hello. Is there a way to retrieve a list of snps from Affymetirx microarray files, such as cychp, CEL

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Question: snp list from Affymetirx microarray files

Hello. Is there a way to retrieve a list of snps from Affymetirx microarray files, such as cychp, CEL

2/23/21

Mirko Pisati, Henrik Bengtsson3

11/13/20

Error with process function: package sfit not found

Hi, thanks for your help, now the package works. Yesterday among the various attempts I made I ran

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Error with process function: package sfit not found

Hi, thanks for your help, now the package works. Yesterday among the various attempts I made I ran

11/13/20

Sreya Mukherjee, Pierre Neuvial2

11/1/19

cant get aroma to load

Thanks for reporting. Retry with: if (.Platform$OS.type == "windows") options(url.method =

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cant get aroma to load

Thanks for reporting. Retry with: if (.Platform$OS.type == "windows") options(url.method =

11/1/19

thomas.g...@merckgroup.com

3/11/19

writeRegions of poor SNP6 arrays failed

Dear Henrik, I segmented SNP6 data of a poor ddata set of ~1200 samples, first with the standard CRMA

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writeRegions of poor SNP6 arrays failed

Dear Henrik, I segmented SNP6 data of a poor ddata set of ~1200 samples, first with the standard CRMA

3/11/19

thomas.g...@merckgroup.com, Henrik Bengtsson3

9/13/18

CalMaTe model fitting error

Hi. This is a hard-to-troubleshoot problem. This could be due to one or more arrays having weak/noisy

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CalMaTe model fitting error

Hi. This is a hard-to-troubleshoot problem. This could be due to one or more arrays having weak/noisy

9/13/18

8/4/18

GcRMaBackgroundCorrection problem with HTA2.0

Dear Henrik, I am trying to run GcRMaBackgroundCorrection on HTA2.0 arrays. I built my own probeflat

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GcRMaBackgroundCorrection problem with HTA2.0

Dear Henrik, I am trying to run GcRMaBackgroundCorrection on HTA2.0 arrays. I built my own probeflat

8/4/18

Fred Foucault, … ck...@ebi.ac.uk9

5/30/18

ACNE getGenomeInformation(cdf) failed

Hi Henrik, Very similar to the issue above, I have checked the file size, which is fine. However this

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ACNE getGenomeInformation(cdf) failed

Hi Henrik, Very similar to the issue above, I have checked the file size, which is fine. However this

5/30/18

jjspring OH, Sanjeev Sariya3

4/17/18

transcript and exon level analysis for detection of alternative splicings

Hi Sunghee, Did you figure this out? I'm in the same boat. On Sunday, 21 September 2014 22:19:09

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transcript and exon level analysis for detection of alternative splicings

Hi Sunghee, Did you figure this out? I'm in the same boat. On Sunday, 21 September 2014 22:19:09

4/17/18

Sanjeev Sariya2

4/16/18

RmaPlm and ExonRmaPlm

Please suggest. ------------- On Thursday, 12 April 2018 10:43:46 UTC-4, Sanjeev Sariya wrote: Hello

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RmaPlm and ExonRmaPlm

Please suggest. ------------- On Thursday, 12 April 2018 10:43:46 UTC-4, Sanjeev Sariya wrote: Hello

4/16/18

1/19/18

CytoscanHD array cdf file for b38/hg38

Hello, I am trying to use Aroma package to analyse CNVs from CytoscanHD array. I have only found the

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CytoscanHD array cdf file for b38/hg38

Hello, I am trying to use Aroma package to analyse CNVs from CytoscanHD array. I have only found the

1/19/18

Pabita Saud, Henrik Bengtsson3

12/22/17

Re: [aroma.affymetrix] Error using RMA

Thank you. Best Regards, Pabita On Fri, Dec 22, 2017 at 12:02 PM, Henrik Bengtsson <henrik.

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Re: [aroma.affymetrix] Error using RMA

Thank you. Best Regards, Pabita On Fri, Dec 22, 2017 at 12:02 PM, Henrik Bengtsson <henrik.

12/22/17

Karyn Meltz Steinberg, Henrik Bengtsson3

12/19/17

Error writing to connection

Thank you so much--Number 1 was indeed the issue. I truly appreciate your quick response. Best, KMS

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Error writing to connection

Thank you so much--Number 1 was indeed the issue. I truly appreciate your quick response. Best, KMS

12/19/17

wxp...@gmail.com, … Henrik Bengtsson7

11/24/17

Error: object 'csC' not found.

If you called csC <- process(acc, verbose=verbose) and csC is not found, then there was an error

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Error: object 'csC' not found.

If you called csC <- process(acc, verbose=verbose) and csC is not found, then there was an error

11/24/17

11/13/17

object csC not found

I was working with the cytoScan HD chiptype to preprocess the .CEL files But was inturrupted with the

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object csC not found

I was working with the cytoScan HD chiptype to preprocess the .CEL files But was inturrupted with the

11/13/17

10/17/17

Using Perl script to create flat file

Hi, I am using convertProbesetCSV_differentInput.pl file (http://www.aroma-project.org/share/scripts/

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Using Perl script to create flat file

Hi, I am using convertProbesetCSV_differentInput.pl file (http://www.aroma-project.org/share/scripts/

10/17/17

Emanuel Gonçalves, Henrik Bengtsson6

9/1/17

CbsModel or writeRegions error

I've been trying to figure where the error could show up and I have some "poor" guesses

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CbsModel or writeRegions error

I've been trying to figure where the error could show up and I have some "poor" guesses

9/1/17

mbaudis, … Francesca Scellato14

7/12/17

Affymetrix Oncoscan library files

Thank you all for your answers. I was able to export from Nexus the segment, probes and snps file for

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Affymetrix Oncoscan library files

Thank you all for your answers. I was able to export from Nexus the segment, probes and snps file for

7/12/17

Emanuel Gonçalves, Henrik Bengtsson7

6/22/17

CBS input dataframe

Hi, This seems to be working well, although I'm concerned with the raw counts distributions of

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CBS input dataframe

Hi, This seems to be working well, although I'm concerned with the raw counts distributions of

6/22/17

4/13/17

CalMaTe running error with function "divideBy"

Hi Henrik, I'm using doASCRMAv2() and then CalMaTe package on a SNP array 6.0 series. I use the

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CalMaTe running error with function "divideBy"

Hi Henrik, I'm using doASCRMAv2() and then CalMaTe package on a SNP array 6.0 series. I use the

4/13/17

Sophie Marion de Procé

4/7/17

Gene ST array summarisation by probeset?

Dear all, I'm analysing a Rat Gene ST 2.1 array. I would like to filter the dataset using

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Gene ST array summarisation by probeset?

Dear all, I'm analysing a Rat Gene ST 2.1 array. I would like to filter the dataset using

4/7/17

Sophie Marion de Procé, Hooiveld, Guido3

4/5/17

AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

Dear Guido, Thank you for your reply, I followed your much simpler code and it worked! So it seems I

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AffymetrixCdfFile$byChipType -- Argument 'nbrOfUnits' contains 1 NA value(s)

Dear Guido, Thank you for your reply, I followed your much simpler code and it worked! So it seems I

4/5/17

Henrik Bengtsson

3/24/17

aroma.affymetrix 3.1.0 release

aroma.affymetrix 3.1.0 and friends have been updated and are being rolled out on CRAN. These days I

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aroma.affymetrix 3.1.0 release

aroma.affymetrix 3.1.0 and friends have been updated and are being rolled out on CRAN. These days I

3/24/17

Renuka Kandhaya Pillai, Guido3

3/7/17

How to extract .CEL files from .DTT file

Thank you very much Guido, I tried renaming the .DTT file to .ZIP. But the renamed ZIP is damaged/

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How to extract .CEL files from .DTT file

Thank you very much Guido, I tried renaming the .DTT file to .ZIP. But the renamed ZIP is damaged/

3/7/17

Gaius Augustus, Amy Sherborne2

11/1/16

Running multiple pairs through Paired PSCBS

Hi Gaius, I have just written an R script to do exactly the thing you you are asking about, I hope it

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Running multiple pairs through Paired PSCBS

Hi Gaius, I have just written an R script to do exactly the thing you you are asking about, I hope it

11/1/16

thomas.g...@merckgroup.com, Henrik Bengtsson4

8/7/16

troubles in doing PCR fragment length normalization AROMA3.0

Hi, and sorry for the delay. 1. Yes, it could certainly be that the problem was introduced recently.

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troubles in doing PCR fragment length normalization AROMA3.0

Hi, and sorry for the delay. 1. Yes, it could certainly be that the problem was introduced recently.

8/7/16

Marijke VAN MOERBEKE, Henrik Bengtsson2

8/7/16

Error while setting up AffymetrixCelSet

Hmm... this looks weird but as usual, there's probably a simple explanation to it. Yes, it could

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Error while setting up AffymetrixCelSet

Hmm... this looks weird but as usual, there's probably a simple explanation to it. Yes, it could

8/7/16

7/12/16

Using aroma.affymetrix to perform QC

Hello: I am new to the aroma project and needed help on how to use it to perform QC on Affy samples.

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Using aroma.affymetrix to perform QC

Hello: I am new to the aroma project and needed help on how to use it to perform QC on Affy samples.

7/12/16

roman....@googlemail.com, Henrik Bengtsson8

7/8/16

CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

Hi, it's me again and I have good news: It seems like it was simply an issue with the sample (

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CytoScanHD_Array: problems with CbsModel(), 'Failed to locate Class object for class 'FutureError'

Hi, it's me again and I have good news: It seems like it was simply an issue with the sample (

7/8/16

Gaius Augustus, Henrik Bengtsson2

5/13/16

"Error: Failed to retrieve genome information" + paired samples

Hi, comments below. On Fri, May 13, 2016 at 10:24 AM, Gaius Augustus <gaiusja...@gmail.com>

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"Error: Failed to retrieve genome information" + paired samples

Hi, comments below. On Fri, May 13, 2016 at 10:24 AM, Gaius Augustus <gaiusja...@gmail.com>

5/13/16

Kevin McCormick, Henrik Bengtsson2

4/23/16

Incorporating Tumor Purity for ASCRMA / PSCBS

In the PSCBS package, we provide the `estimateKappa()` function for estimating kappa, which we refer

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Incorporating Tumor Purity for ASCRMA / PSCBS

In the PSCBS package, we provide the `estimateKappa()` function for estimating kappa, which we refer

4/23/16

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