We have also looked into the C-code (simpleaffy v1.09) and found the
(1) On line 547:
According to us the chip is being remapped onto a grid. Hence, if the
of columns or rows of the affy-chip respectively devided by the number
columns or rows of the grid does not yield an integer, then the number
rows/columns to be places in each cell of the grid was rounded down
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
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
these lines are wrong as "nrow" and "ncol" don't respectively
"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
chips resulting from the calculations of the simpleaffy v1.0 and
v1.09. The results were quite comparable, except for 54 values that
by more than 0.1 units (on log scale) and ranged from -1.635837 to
Rudy van Eijsden.
Cluster of Genetics and Cell Biology
Department of Clinical Genetics
Universiteitssingel 50, Room No 5.140
6229 ER Maastricht
P.O. box 616, post-box 16
6200 MD Maastricht
+31 (0)43 3881916 (Office)
+31 (0)43 3881995 (Secretariat)
+31 (0)43 3884573
E-mail & Internet
From: Crispin Miller [mailto:CMiller@PICR.man.ac.uk]
Sent: Tuesday, May 11, 2004 12:28 PM
Subject: RE: [BioC] Error doing Mas5 calculation with Simpleaffy
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...
[mailto:firstname.lastname@example.org] On Behalf Of
Sent: 07 May 2004 13:37
Subject: [BioC] Error doing Mas5 calculation with Simpleaffy package
I get the following error when doing the Mas5 calculation using the
Rgui.exe has generated errors and will be closed by Windows. You will
need to restart the program.
An error log is being created.
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)
>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 <-
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.
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