limma and spottypes

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Simon Melov ▴ 340

@simon-melov-266

Last seen 9.6 years ago

Hi, I'm trying to plot some spottypes described in the usersguide of limma (section 4.6). Unfortunately, I dont seem to be able to do this if I follow the instructions in the guide. Here is the input and output > spottypes<-readSpotTypes() > spottypes SpotType ID Name Color 1 gene * * Black 2 Calibration-1 Spot Report Product 1 * red 3 Calibration-2 Spot Report Product 10 * red 4 Calibration-3 Spot Report Product 2 * red 5 Calibration-4 Spot Report Product 3 * red 6 Calibration-5 Spot Report Product 4 * red 7 Calibration-6 Spot Report Product 5 * red 8 Calibration-7 Spot Report Product 6 * red 9 Calibration-8 Spot Report Product 7 * red 10 Calibration-9 Spot Report Product 8 * red 11 Calibration-10 Spot Report Product 9 * red 12 Empty Empty * yellow 13 Buffer 3XSSC 1.5M Betaine * blue 14 No data No data * pink 15 Human Cot Human Cot 1 * green 16 Mouse Cot Mouse Cot 1 * green 17 B Actin B-Human Actin * purple 18 Poly A Poly A * orange 19 Salmon Sperm Salmon Sperm * orange > RG$genes$Status<-spotStatus(spottypes) Error: couldn't find function "spotStatus" > In addition, I dont seem to be able to find any mention of a "spotStatus" function via search. Any help would be appreciated. thanks Simon. -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1730 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20031221/3dacbd39/attachment.bin

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ADD COMMENT • link 20.4 years ago Simon Melov ▴ 340

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Ken Simpson ▴ 70

@ken-simpson-520

Last seen 9.6 years ago

Hi Simon, Looks like that part of the user guide is out of date. controlStatus() should do what you want. (do help.start(), then click on Packages and then limma, and consult section 3: ReadingData) Cheers, Ken On Sun, 21 Dec 2003, Simon Melov wrote: > Hi, > I'm trying to plot some spottypes described in the usersguide of limma > (section 4.6). Unfortunately, I dont seem to be able to do this if I > follow the instructions in the guide. > > Here is the input and output > > > spottypes<-readSpotTypes() > > spottypes > SpotType ID Name Color > 1 gene * * Black > 2 Calibration-1 Spot Report Product 1 * red > 3 Calibration-2 Spot Report Product 10 * red > 4 Calibration-3 Spot Report Product 2 * red > 5 Calibration-4 Spot Report Product 3 * red > 6 Calibration-5 Spot Report Product 4 * red > 7 Calibration-6 Spot Report Product 5 * red > 8 Calibration-7 Spot Report Product 6 * red > 9 Calibration-8 Spot Report Product 7 * red > 10 Calibration-9 Spot Report Product 8 * red > 11 Calibration-10 Spot Report Product 9 * red > 12 Empty Empty * yellow > 13 Buffer 3XSSC 1.5M Betaine * blue > 14 No data No data * pink > 15 Human Cot Human Cot 1 * green > 16 Mouse Cot Mouse Cot 1 * green > 17 B Actin B-Human Actin * purple > 18 Poly A Poly A * orange > 19 Salmon Sperm Salmon Sperm * orange > > RG$genes$Status<-spotStatus(spottypes) > Error: couldn't find function "spotStatus" > > > > In addition, I dont seem to be able to find any mention of a > "spotStatus" function via search. > > Any help would be appreciated. > > thanks > > Simon.

ADD COMMENT • link 20.4 years ago Ken Simpson ▴ 70

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Gordon Smyth 50k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

Simon, As Ken says, spotStatus() has been replaced by controlStatus(). Be careful also with the syntax: two arguments are required. You can upgrade limma from http://bioinf.wehi.edu.au/limma to get the corrected User Guide. (Don't upgrade from the BioC development area because development limma now depends on R 1.9.0dev.) Cheers Gordon At 02:18 PM 22/12/2003, Ken Simpson wrote: >Hi Simon, > >Looks like that part of the user guide is out of date. controlStatus() >should do what you want. (do help.start(), then click on Packages and >then limma, and consult section 3: ReadingData) > >Cheers, > >Ken > >On Sun, 21 Dec 2003, Simon Melov wrote: > > > Hi, > > I'm trying to plot some spottypes described in the usersguide of limma > > (section 4.6). Unfortunately, I dont seem to be able to do this if I > > follow the instructions in the guide. > > > > Here is the input and output > > > > > spottypes<-readSpotTypes() > > > spottypes > > SpotType ID Name Color > > 1 gene * * Black > > 2 Calibration-1 Spot Report Product 1 * red > > 3 Calibration-2 Spot Report Product 10 * red > > 4 Calibration-3 Spot Report Product 2 * red > > 5 Calibration-4 Spot Report Product 3 * red > > 6 Calibration-5 Spot Report Product 4 * red > > 7 Calibration-6 Spot Report Product 5 * red > > 8 Calibration-7 Spot Report Product 6 * red > > 9 Calibration-8 Spot Report Product 7 * red > > 10 Calibration-9 Spot Report Product 8 * red > > 11 Calibration-10 Spot Report Product 9 * red > > 12 Empty Empty * yellow > > 13 Buffer 3XSSC 1.5M Betaine * blue > > 14 No data No data * pink > > 15 Human Cot Human Cot 1 * green > > 16 Mouse Cot Mouse Cot 1 * green > > 17 B Actin B-Human Actin * purple > > 18 Poly A Poly A * orange > > 19 Salmon Sperm Salmon Sperm * orange > > > RG$genes$Status<-spotStatus(spottypes) > > Error: couldn't find function "spotStatus" > > > > > > > In addition, I dont seem to be able to find any mention of a > > "spotStatus" function via search. > > > > Any help would be appreciated. > > > > thanks > > > > Simon. > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

ADD COMMENT • link 20.4 years ago Gordon Smyth 50k

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Simon Melov ▴ 340

@simon-melov-266

Last seen 9.6 years ago

Thanks for the speedy response. After upgrading to the latest version of limma it works fine. However, I now would like to just plot some spots from the spot types file. I'm sure its pretty simple, but Ive tried all sorts of permutations of the controlStatus function, but cant seem to get it to work. Here is an example, I would like to just plot "genes", as well as "Buffer" in an MA plot for example. I already assigned colors in the spottype file. What would be the appropriate functions? thanks Simon. >types<-readSpotTypes() > types SpotType ID Name Color 1 gene * * Black 2 Calibration-1 Spot Report Product 1 * red 3 Calibration-2 Spot Report Product 10 * red 4 Calibration-3 Spot Report Product 2 * red 5 Calibration-4 Spot Report Product 3 * red 6 Calibration-5 Spot Report Product 4 * red 7 Calibration-6 Spot Report Product 5 * red 8 Calibration-7 Spot Report Product 6 * red 9 Calibration-8 Spot Report Product 7 * red 10 Calibration-9 Spot Report Product 8 * red 11 Calibration-10 Spot Report Product 9 * red 12 Empty Empty * yellow 13 Buffer 3XSSC 1.5M Betaine * blue 14 No data No data * pink 15 Human Cot Human Cot 1 * green 16 Mouse Cot Mouse Cot 1 * green 17 B Actin B-Human Actin * purple 18 Poly A Poly A * orange 19 Salmon Sperm Salmon Sperm * orange > RG$genes$Status<-controlStatus(types,RG) Matching patterns for: ID Name Found 25088 gene Found 32 Calibration-1 Found 32 Calibration-2 Found 32 Calibration-3 Found 32 Calibration-4 Found 32 Calibration-5 Found 32 Calibration-6 Found 32 Calibration-7 Found 32 Calibration-8 Found 32 Calibration-9 Found 32 Calibration-10 Found 512 Empty Found 288 Buffer Found 0 No data Found 32 Human Cot Found 32 Mouse Cot Found 32 B Actin Found 32 Poly A Found 32 Salmon Sperm Setting attributes: values Color > plotMA(RG) -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 2565 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20031221/58265bd9/attachment-0001.bin

ADD COMMENT • link 20.4 years ago Simon Melov ▴ 340

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At 05:58 PM 22/12/2003, Simon Melov wrote: >Thanks for the speedy response. After upgrading to the latest version of >limma it works fine. However, I now would like to just plot some spots >from the spot types file. I'm sure its pretty simple, but Ive tried all >sorts of permutations of the controlStatus function, but cant seem to get >it to work. Here is an example, I would like to just plot "genes", as well >as "Buffer" in an MA plot for example. I already assigned colors in the >spottype file. What would be the appropriate functions? Don't change the controlStatus function, just use plotMA(RG,value=c("gene","Buffer"),col=c("black","blue")) General rule: controlStatus sets permanent attributes, but you can over-ride them by specifying values, colors etc explicitly. Another way to achieve the same thing would be to temporarily subset the RG object. Gordon >thanks > >Simon. > >types<-readSpotTypes() > > types > SpotType ID Name Color >1 gene * * Black >2 Calibration-1 Spot Report Product 1 * red >3 Calibration-2 Spot Report Product 10 * red >4 Calibration-3 Spot Report Product 2 * red >5 Calibration-4 Spot Report Product 3 * red >6 Calibration-5 Spot Report Product 4 * red >7 Calibration-6 Spot Report Product 5 * red >8 Calibration-7 Spot Report Product 6 * red >9 Calibration-8 Spot Report Product 7 * red >10 Calibration-9 Spot Report Product 8 * red >11 Calibration-10 Spot Report Product 9 * red >12 Empty Empty * yellow >13 Buffer 3XSSC 1.5M Betaine * blue >14 No data No data * pink >15 Human Cot Human Cot 1 * green >16 Mouse Cot Mouse Cot 1 * green >17 B Actin B-Human Actin * purple >18 Poly A Poly A * orange >19 Salmon Sperm Salmon Sperm * orange > > RG$genes$Status<-controlStatus(types,RG) >Matching patterns for: ID Name >Found 25088 gene >Found 32 Calibration-1 >Found 32 Calibration-2 >Found 32 Calibration-3 >Found 32 Calibration-4 >Found 32 Calibration-5 >Found 32 Calibration-6 >Found 32 Calibration-7 >Found 32 Calibration-8 >Found 32 Calibration-9 >Found 32 Calibration-10 >Found 512 Empty >Found 288 Buffer >Found 0 No data >Found 32 Human Cot >Found 32 Mouse Cot >Found 32 B Actin >Found 32 Poly A >Found 32 Salmon Sperm >Setting attributes: values Color > > plotMA(RG)

ADD REPLY • link 20.4 years ago Gordon Smyth 50k

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