Question: Error doing Mas5 calculation with Simpleaffy package
0
gravatar for Rudy.vanEijsden@GEN.unimaas.nl
15.5 years ago by
Dear all, I get the following error when doing the Mas5 calculation using the Simpleaffy package: ============================================================ Rgui.exe has generated errors and will be closed by Windows. You will need to restart the program. An error log is being created. ============================================================ More details: R-version: 1090 for Windows. Simpleaffy version: Version: 1.09, Packaged: Fri Apr 16 03:23:08 2004; madman Chips: 4 affymetrix yeast chips (YG-S98) Code used: >library(simpleaffy) >library(ygs98cdf) >raw.data <- read.affy() >data.mas <- call.exprs(raw.data, "mas5") This is the moment when the error pups up. Using rma in stead of mas5 does not give an error (>data.rma <- call.exprs(raw.data, "rma") Do you have any idea how to solve this problem. I have tried doing the mas5 calculation using the affy package....and this works fine. But I would like to use the simpleaffy package. Greetz, Rudy. rudy.vaneijsden@gen.unimaas.nl
yeast affy simpleaffy • 506 views
ADD COMMENTlink modified 15.4 years ago by Crispin Miller1.1k • written 15.5 years ago by Rudy.vanEijsden@GEN.unimaas.nl50
Answer: Error doing Mas5 calculation with Simpleaffy package
0
gravatar for Crispin Miller
15.5 years ago by
Crispin Miller1.1k
Crispin Miller1.1k wrote:
Hi Rudy, Sounds like a bug in the C library somewhere... I'm just pulling down some yeast chips to play with - I'll get back to you when I've identified the problem... Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Rudy.vanEijsden@gen.unimaas.nl Sent: 07 May 2004 13:37 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Error doing Mas5 calculation with Simpleaffy package Dear all, I get the following error when doing the Mas5 calculation using the Simpleaffy package: ============================================================ Rgui.exe has generated errors and will be closed by Windows. You will need to restart the program. An error log is being created. ============================================================ More details: R-version: 1090 for Windows. Simpleaffy version: Version: 1.09, Packaged: Fri Apr 16 03:23:08 2004; madman Chips: 4 affymetrix yeast chips (YG-S98) Code used: >library(simpleaffy) >library(ygs98cdf) >raw.data <- read.affy() >data.mas <- call.exprs(raw.data, "mas5") This is the moment when the error pups up. Using rma in stead of mas5 does not give an error (>data.rma <- call.exprs(raw.data, "rma") Do you have any idea how to solve this problem. I have tried doing the mas5 calculation using the affy package....and this works fine. But I would like to use the simpleaffy package. Greetz, Rudy. rudy.vaneijsden@gen.unimaas.nl _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
ADD COMMENTlink written 15.5 years ago by Crispin Miller1.1k
Answer: Error doing Mas5 calculation with Simpleaffy package
0
gravatar for Rudy.vanEijsden@GEN.unimaas.nl
15.4 years ago by
Hi Crispin, We have also looked into the C-code (simpleaffy v1.09) and found the following errors: (1) On line 547: According to us the chip is being remapped onto a grid. Hence, if the number of columns or rows of the affy-chip respectively devided by the number of columns or rows of the grid does not yield an integer, then the number of rows/columns to be places in each cell of the grid was rounded down instead of up. This resulted in memory crashes. (2) On lines 515 and 602: According to us the index for the raw and corrected intensities are wrong as c-code start counting at 0 and not 1, therefore the index needs to be decreased by 1. (3) On lines 506 and 507: According to us all the variable related to "x" and "y" respectively correspond to columns and rows. Therefore if the affy-chip is not square these lines are wrong as "nrow" and "ncol" don't respectively correspond to "y" and "x". Attached you will find a patch for the "simpleaffy2.c" source file. After these corrections we have compared the MAS5 expression values of 4 chips resulting from the calculations of the simpleaffy v1.0 and simpleaffy v1.09. The results were quite comparable, except for 54 values that differed by more than 0.1 units (on log scale) and ranged from -1.635837 to 1.448547 units. Greetings, Rudy van Eijsden. Maastricht University Cluster of Genetics and Cell Biology Department of Clinical Genetics Visiting Address Universiteitssingel 50, Room No 5.140 6229 ER Maastricht The Netherlands Postal Address P.O. box 616, post-box 16 6200 MD Maastricht The Netherlands Telephone +31 (0)43 3881916 (Office) +31 (0)43 3881995 (Secretariat) Fax +31 (0)43 3884573 E-mail & Internet rudy.vaneijsden@gen.unimaas.nl http://www.gen.unimaas.nl <http: www.gen.unimaas.nl=""/> -----Original Message----- From: Crispin Miller [mailto:CMiller@PICR.man.ac.uk] Sent: Tuesday, May 11, 2004 12:28 PM To: Rudy.vanEijsden@gen.unimaas.nl Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] Error doing Mas5 calculation with Simpleaffy package Hi Rudy, Sounds like a bug in the C library somewhere... I'm just pulling down some yeast chips to play with - I'll get back to you when I've identified the problem... Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Rudy.vanEijsden@gen.unimaas.nl Sent: 07 May 2004 13:37 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Error doing Mas5 calculation with Simpleaffy package Dear all, I get the following error when doing the Mas5 calculation using the Simpleaffy package: ============================================================ Rgui.exe has generated errors and will be closed by Windows. You will need to restart the program. An error log is being created. ============================================================ More details: R-version: 1090 for Windows. Simpleaffy version: Version: 1.09, Packaged: Fri Apr 16 03:23:08 2004; madman Chips: 4 affymetrix yeast chips (YG-S98) Code used: >library(simpleaffy) >library(ygs98cdf) >raw.data <- read.affy() >data.mas <- call.exprs(raw.data, "mas5") This is the moment when the error pups up. Using rma in stead of mas5 does not give an error (>data.rma <- call.exprs(raw.data, "rma") Do you have any idea how to solve this problem. I have tried doing the mas5 calculation using the affy package....and this works fine. But I would like to use the simpleaffy package. Greetz, Rudy. rudy.vaneijsden@gen.unimaas.nl _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use of the person(s) ('the intended recipient') to whom it was addressed. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Paterson Institute for Cancer Research or the Christie Hospital NHS Trust. It may contain information that is privileged & confidential within the meaning of applicable law. Accordingly any dissemination, distribution, copying, or other use of this message, or any of its contents, by any person other than the intended recipient may constitute a breach of civil or criminal law and is strictly prohibited. If you are NOT the intended recipient please contact the sender and dispose of this e-mail as soon as possible. -------------- next part -------------- A non-text attachment was scrubbed... Name: simpleaffy2.patch Type: application/octet-stream Size: 3253 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040525/162cc253/simpleaffy2.obj
ADD COMMENTlink written 15.4 years ago by Rudy.vanEijsden@GEN.unimaas.nl50
Answer: Error doing Mas5 calculation with Simpleaffy package
0
gravatar for Crispin Miller
15.4 years ago by
Crispin Miller1.1k
Crispin Miller1.1k wrote:
Thanks Rudy, I'll have a look into things and produce an update as soon as I can, hopefully in the next day or two... Whilst I'm at it, I'll add the 4302 chips into the QC stuff... In the meantime, I strongly suggest treating the mas5 calls in simpleaffy with caution. :-( Regards, Crispin -----Original Message----- From: Rudy.vanEijsden@GEN.unimaas.nl [mailto:Rudy.vanEijsden@GEN.unimaas.nl] Sent: 25 May 2004 15:16 To: Crispin Miller Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] Error doing Mas5 calculation with Simpleaffy package Hi Crispin, We have also looked into the C-code (simpleaffy v1.09) and found the following errors: (1) On line 547: According to us the chip is being remapped onto a grid. Hence, if the number of columns or rows of the affy-chip respectively devided by the number of columns or rows of the grid does not yield an integer, then the number of rows/columns to be places in each cell of the grid was rounded down instead of up. This resulted in memory crashes. (2) On lines 515 and 602: According to us the index for the raw and corrected intensities are wrong as c-code start counting at 0 and not 1, therefore the index needs to be decreased by 1. (3) On lines 506 and 507: According to us all the variable related to "x" and "y" respectively correspond to columns and rows. Therefore if the affy-chip is not square these lines are wrong as "nrow" and "ncol" don't respectively correspond to "y" and "x". Attached you will find a patch for the "simpleaffy2.c" source file. After these corrections we have compared the MAS5 expression values of 4 chips resulting from the calculations of the simpleaffy v1.0 and simpleaffy v1.09. The results were quite comparable, except for 54 values that differed by more than 0.1 units (on log scale) and ranged from -1.635837 to 1.448547 units. Greetings, Rudy van Eijsden. Maastricht University Cluster of Genetics and Cell Biology Department of Clinical Genetics Visiting Address Universiteitssingel 50, Room No 5.140 6229 ER Maastricht The Netherlands Postal Address P.O. box 616, post-box 16 6200 MD Maastricht The Netherlands Telephone +31 (0)43 3881916 (Office) +31 (0)43 3881995 (Secretariat) Fax +31 (0)43 3884573 E-mail & Internet rudy.vaneijsden@gen.unimaas.nl http://www.gen.unimaas.nl <http: www.gen.unimaas.nl=""/> -----Original Message----- From: Crispin Miller [mailto:CMiller@PICR.man.ac.uk] Sent: Tuesday, May 11, 2004 12:28 PM To: Rudy.vanEijsden@gen.unimaas.nl Cc: bioconductor@stat.math.ethz.ch Subject: RE: [BioC] Error doing Mas5 calculation with Simpleaffy package Hi Rudy, Sounds like a bug in the C library somewhere... I'm just pulling down some yeast chips to play with - I'll get back to you when I've identified the problem... Cheers, Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Rudy.vanEijsden@gen.unimaas.nl Sent: 07 May 2004 13:37 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Error doing Mas5 calculation with Simpleaffy package Dear all, I get the following error when doing the Mas5 calculation using the Simpleaffy package: ============================================================ Rgui.exe has generated errors and will be closed by Windows. You will need to restart the program. An error log is being created. ============================================================ More details: R-version: 1090 for Windows. Simpleaffy version: Version: 1.09, Packaged: Fri Apr 16 03:23:08 2004; madman Chips: 4 affymetrix yeast chips (YG-S98) Code used: >library(simpleaffy) >library(ygs98cdf) >raw.data <- read.affy() >data.mas <- call.exprs(raw.data, "mas5") This is the moment when the error pups up. Using rma in stead of mas5 does not give an error (>data.rma <- call.exprs(raw.data, "rma") Do you have any idea how to solve this problem. I have tried doing the mas5 calculation using the affy package....and this works fine. But I would like to use the simpleaffy package. Greetz, Rudy. rudy.vaneijsden@gen.unimaas.nl _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
ADD COMMENTlink written 15.4 years ago by Crispin Miller1.1k
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