[BioC] spotTypes function not available in limma?

V.C.L. de Jager v.dejager at erasmusmc.nl
Tue Apr 27 09:09:01 CEST 2004

Dear madam, sir,

I am using Limma with the latest version of bioconductor.

After succesfull loading of my Imagene files I want to load a file called
SpotTypes.txt as outlined in the Limma usermanual on page 6.
Reading the spottypes goes well, but when I apply the spotStatus function I
get the following error message:

	> RG$genes$Status <- spotStatus(spottypes)
	Error: couldn't find function "spotStatus"

If I leave out the spottypes I can create MA plots etc.
I'm rather new to R so sometimes I'm puzzled if it is something I do wrong
or if something is broken in the package.
Could you tell me if this is a bug in Limma or if it is my fault.

This is the order of things I do. I attached the SpotTypes.txt file

#read the imagene files
RG <- read.imagene(files)

#set the spottypes
spottypes <- readSpotTypes()

RG$genes$status <- spotStatus(spottypes) # this goes wrong

best regards
Victor de Jager

M.Sc. V.C.L. de Jager
Erasmus MC, dept of bioinformatics
Dr. Molewaterplein 50
3015 GE Rotterdam

tel: 31-10-4088454
fax: 31-10-4089468
email: v.dejager at erasmusmc.nl
-------------- next part --------------
SpotType	ID	Name	Color
Oligo	*	*	black
Stratagene - Alien Oligo 1	*	ECB_MOUSECTRL_00001_01	red
Stratagene - Alien Oligo 2	*	ECB_MOUSECTRL_00001_02	red
Stratagene - Alien Oligo 3	*	ECB_MOUSECTRL_00001_03	red
Stratagene - Alien Oligo 4	*	ECB_MOUSECTRL_00001_04	red
Stratagene - Alien Oligo 5	*	ECB_MOUSECTRL_00001_05	red
Stratagene - Alien Oligo 6	*	ECB_MOUSECTRL_00001_06	red
Stratagene - Alien Oligo 7	*	ECB_MOUSECTRL_00001_07	red
Stratagene - Alien Oligo 8	*	ECB_MOUSECTRL_00001_08	red
Stratagene - Alien Oligo 9	*	ECB_MOUSECTRL_00001_09	red
Stratagene - Alien Oligo 10	*	ECB_MOUSECTRL_00001_10	red
Cot-1 DNA	*	ECB_MOUSECTRL_00001_11	brown
Spot Buffer	*	ECB_MOUSECTRL_00001_12	brown
Poly dA	*	ECB_MOUSECTRL_00001_13	brown
Salmon Sperm DNA	*	ECB_MOUSECTRL_00001_14	brown
M13-Cy3 Oligo Landmark	*	ECB_MOUSECTRL_00001_15	blue

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