[BioC] Memory issues with limma and ImaGen file import

[CV Markus]

Hallo Christian,

ich hab genau dasselbe Problem, bei mir kommt die Meldung:

"Fehler: kann Vektor der Größe 7179 Kb nicht allozieren"

Am mem.limit() kann es nicht liegen, denn dann würde eine Meldung kommen, die darauf hinweist, dass das Speichermaximum erreicht ist.
An der Art, wie die Daten eingelesen werden, kann es auch nicht liegen, ich verwende z.B. keine Textdateien, sondern eine Datenbankabfrage per ODBC und habe trotzdem das Problem.

Hat sich das Problem bei Dir inzwischen gelöst?

Grüße, Markus Preisetanz

Christian Spieth Wrote:
-----------------------------
[BioC] Memory issues with limma and ImaGen file import
Christian Spieth Christian.Spieth at uni-tuebingen.de
Fri Apr 28 16:21:43 CEST 2006

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Hi,

I am having a problem with limma 2.4.13 and ImaGene files: 
Whenever I try to read the files as described in the manual

targets <- readTargets()
files <- targets[,c("FileNameCy3","FileNameCy5")]
RG <- read.maimages(files, source ="imagene")

R aborts the operation with the following error message:

> RG <- read.maimages(files,source="imagene")
Read header information
Fehler: kann Vektor der Größe 3200000 Kb nicht allozieren 
(Error: unable to allocate a vector of size 3200000 Kb) 

I am trying to read 10 chip files ( 5 replication with red and green). 
Each file is approx. 6MB. Is there a special format of the ImaGene files?
My files start with


Begin Header
	version	5.6.1
	Date	Mon Apr 24 20:13:17 CEST 2006
	Image File
X:\Lab_Hochholdinger\Individual_folders\Diana\microarray\lrt\replicate1\01Mu
rot\0G701Murot.tif
	Page	0
	Page Name	
	Inverted	false
	Begin Field Dimensions
		Field	Metarows	Metacols	Rows	Cols
		A	8	4	20	20
		B	4	4	20	20
	End Field Dimensions
	Begin Measurement parameters
		Segmentation Method	auto
		Signal Low	0.0
		Signal High	0.0
		Background Low	0.0
		Background High	0.0
		Background Buffer	3.0
		Background Width	5.0
	End Measurement parameters
	Begin Alerts
		Control Type	Minimum threshold	If tested
Percentage allowed	If failed	Maximum threshold	If tested
Percentage allowed	If failed	CV threshold	If tested	If
failed
	End Alerts
	Begin Quality settings
		Empty Spots	true	Threshold:	2.0
		Poor Spots	true
		Begin Poor Spots Parameters
			Background contamination flag	true	Threshold:
0.9995
			Background tested against subgrid data only	true
			Signal contamination flag	false	Threshold:
0.9995
			Signal contamination test connected to background
contamination threshold	false
			Ignored percentage flag	true	Threshold:	25.0
			Open perimeter flag	true	Threshold:	30.0
			Shape regularity flag	true	Threshold:	0.6
			Area To Perimeter Ratio flag	false	Threshold:
0.7
			Offset flag	true	Threshold:	60.0
		End Poor Spots Parameters
		Negative Spots	true
		
	End Quality settings
End Header
Begin Raw Data
	Field	Meta Row	Meta Column	Row	Column	Gene ID	Flag
Signal Mean	Background Mean	Signal Median	Background Median
Signal Mode	Background Mode	Signal Area	Background Area	Signal Total
Background Total	Signal Stdev	Background Stdev	Shape
Regularity	Ignored Area	Spot Area	Ignored Median	Area To
Perimeter	Open Perimeter	XCoord	YCoord	Diameter	Position
offset	Offset X	Offset Y	Expected X	Expected Y	CM-X
CM-Y	CM Offset	CM Offset-X	CM Offset-Y	Min Diam	Max
Diam	Control	Failed Control	Background contamination present
Signal contamination present	Ignored % failed	Open perimeter
failed	Shape regularity failed	Perim-to-area failed	Offset failed
Empty spot	Negative spot	Selected spot
	A	1	1	1	1	HakeT2_V2-I-13-CB250166	0
6628.6592	637.9275	6496.0	542.0	6694.4912	441.2314
179.0	262.0	1186530.0	167137.0	2784.5909	466.856
0.895	0.0	179.0	null	0.9763	0.0	1898.0	5548.0	16.0
1.824	-0.7266	-1.673	1898.7266	5549.673	1898.3799
5547.8547	1.851	-0.3467	-1.8183	14.7603	15.6522		0	0
0	0	0	0	0	0	0	0	0

......




The error happens both under Windows (1GB RAM) and Linux (4GB RAM). 
Anyone an idea?

Thanks in advance!

christian


--
 Christian Spieth
 Dipl.-Ing., MSc (Oxon)
 Center for Bioinformatics (ZBIT), Univ. Tuebingen
 NGFN - Nationales GenomForschungsNetz 
 Sand 1, D-72076 Tuebingen, Germany
 Phone (+49/0) 7071 29 78987, Fax (+49/0) 7071 29 5091
mailto:christian.spieth at uni-tuebingen.de
 http://www-ra.informatik.uni-tuebingen.de
 
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