[BioC] Error doing Mas5 calculation with Simpleaffy package

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
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 at gen.unimaas.nl
http://www.gen.unimaas.nl <http://www.gen.unimaas.nl/>  

-----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...
Cheers,
Crispin

-----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;
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 at gen.unimaas.nl

_______________________________________________
Bioconductor mailing list
Bioconductor at 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