[BioC] [limma] Possible bug on read.maimages function ?

Marcelo Laia marcelolaia at gmail.com
Sun Sep 20 07:13:30 CEST 2009

I think there is a bug on read.maimages limma function.

I try:

> targets <- readTargets()
> files <- targets[,c("FileNameCy3","FileNameCy5")]
> RG <- read.maimages(files, source="imagene")
Read header information
Read lamina1Cy3_551.txt
Erro em `[.data.frame`(obj, , columns$f) : undefined columns selected

After a lot of time, I try:

> targets <- readTargets()
> files <- targets[,c("FileNameCy3","FileNameCy5")]
> RG <- read.maimages(files, source="imagene",columns=list(f="Signal Median",b="Background Median"))
Read header information
Read lamina1Cy3_551.txt
Read lamina1Cy5_650.txt
Read lamina2Cy3_551.txt
Read lamina2Cy5_650.txt
Read lamina3Cy3_532.txt
Read lamina3Cy5_650.txt
Read lamina5Cy3_532.txt
Read lamina5Cy5_635.txt

Here are more information

> targets
  SlideNumber        FileNameCy3        FileNameCy5  Cy3       Cy5
1           1 lamina1Cy3_551.txt lamina1Cy5_650.txt Pra Banha
2           2 lamina2Cy3_551.txt lamina2Cy5_650.txt Pra Banha
3           3 lamina3Cy3_532.txt lamina3Cy5_650.txt Pra Banha
4           5 lamina5Cy3_532.txt lamina5Cy5_635.txt Pra Banha
> files
         FileNameCy3        FileNameCy5
1 lamina1Cy3_551.txt lamina1Cy5_650.txt
2 lamina2Cy3_551.txt lamina2Cy5_650.txt
3 lamina3Cy3_532.txt lamina3Cy5_650.txt
4 lamina5Cy3_532.txt lamina5Cy5_635.txt

Header of my files

Begin Header

	version	8.0.1

	Date	Thu Jun 11 12:35:08 BRT 2009

	Image File	C:\Users\[snip]\lamina1Cy3_551.tif

	Page	0

	Page Name	

	Inverted	false

	Begin Field Dimensions

		Field	Metarows	Metacols	Rows	Cols

		A	2	2	32	24

		B	2	2	32	24

	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	2.0

		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

		BLANK	0.0	false	1.0%	false	500.0	true	0.1%	false	1.0	false	false

		POSITIVE	1000.0	true	0.1%	false	100000.0	false	1.0%	false	1.0	false	false

	End Alerts

	Begin Quality Flags

		Begin Flagging Settings

			Empty Spots	true	Threshold:	0.96

			Poor Spots	true

			Begin Poor Spots Parameters

				Background contamination flag	true	Threshold:	0.9995

				Background tested against subgrid data only	true

				Signal contamination flag	true	Threshold:	0.9995

				Signal contamination test connected to background contamination
threshold	true

				Ignored percentage flag	true	Threshold:	25.2

				Open perimeter flag	true	Threshold:	20.0

				Shape regularity flag	true	Threshold:	0.6

				Area To Perimeter Ratio flag	false	Threshold:	0.7

				Offset flag	true	Threshold:	60.0

				Saturation flag	true		

			End Poor Spots Parameters

			Negative Spots	true

		End Flagging Settings

		Begin Flagged spots

			# of Empty Spots: 2667

			# of Poor Spots: 288

			# of Negative Spots: 0

			# of Manually Flagged Spots: 0

		End Flagged spots


	End Quality Flags

End Header

Begin Raw Data

	Field	Meta Row	Meta Column	Row	Column	Gene ID	Annotation 1	Annotation
2	Flag	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	Saturated

> sessionInfo()
R version 2.9.2 (2009-08-24)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_2.18.3

loaded via a namespace (and not attached):
[1] tools_2.9.2

Am I doing any mistake?

Thank you very much

Marcelo Luiz de Laia
Universidade do Estado de Santa Catarina
UDESC - www.cav.udesc.br
Lages - SC - Brazil
Linux user number 487797

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