[BioC] Error doing Mas5 calculation with Simpleaffy package

Rudy.vanEijsden at GEN.unimaas.nl Rudy.vanEijsden at GEN.unimaas.nl
Tue May 25 16:16:17 CEST 2004

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


Rudy van Eijsden.

Maastricht University
Cluster of Genetics and Cell Biology
Department of Clinical Genetics

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-----Original Message-----
From: Crispin Miller [mailto:CMiller at PICR.man.ac.uk]
Sent: Tuesday, May 11, 2004 12:28 PM
To: Rudy.vanEijsden at gen.unimaas.nl
Cc: bioconductor at 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...

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
Rudy.vanEijsden at gen.unimaas.nl
Sent: 07 May 2004 13:37
To: bioconductor at 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;
Chips: 4 affymetrix yeast chips (YG-S98)

Code used:
>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.



rudy.vaneijsden at gen.unimaas.nl

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