reading background from imagene output
1
0
Entering edit mode
Matthew Ritchie ▴ 1000
@matthew-ritchie-650
Last seen 19 months ago
Australia
Hi Emanuele, >Hello everybody, >I've noticed that read.maimages doesn't read the same type of value for the signal and the background. If I'm not wrong Imagene output file has three values for them(mean,median and mode); apparently by default read.maimages takes the mean for the signal and the median for the background... > Correct. >For example, how can I extract the median signal and the median background? >I tried not to use the parameters source="imagene" and I've defined the columns of desired values: > >>RG<-read.maimages(files,R="Signal Mean",Rb="Background Mean",G="Signal Mean",Gb="Background mean") >> > >but I got this message: > >Error in read.maimages(files, R = "Signal Mean", Rb = "Background Mean", : > Cannot find column heading in image output file > You're on the right track, however you haven't specified the 'columns' argument correctly in read.maimages(). The following should work. >RG<-read.maimages(files, source="imagene", columns=list(Rf="Signal Mean",Rb="Background Mean",Gf="Signal Mean",Gb="Background mean")) > Best wishes, Matt Ritchie >please somebody help me out! >sorry if once again I bother You with my basic questions... >Thanks in advance. > >Emanuele > [[alternative HTML version deleted]]
• 769 views
ADD COMMENT
0
Entering edit mode
@gordon-smyth
Last seen 10 hours ago
WEHI, Melbourne, Australia
At 02:27 PM 23/03/2004, Matthew Ritchie wrote: >Hi Emanuele, > >> >>Hello everybody, >>I've noticed that read.maimages doesn't read the same type of value for >>the signal and the background. If I'm not wrong Imagene output file has >>three values for them(mean,median and mode); apparently by default >>read.maimages takes the mean for the signal and the median for the >>background... >Correct. >> >>For example, how can I extract the median signal and the median background? >>I tried not to use the parameters source="imagene" and I've defined the >>columns of desired values: >> >>> >>>RG<-read.maimages(files,R="Signal Mean",Rb="Background Mean",G="Signal >>>Mean",Gb="Background mean") >> >> >>but I got this message: >> >>Error in read.maimages(files, R = "Signal Mean", Rb = "Background Mean", : >> Cannot find column heading in image output file >You're on the right track, however you haven't specified the 'columns' >argument correctly in read.maimages(). The following should work. >> >>RG<-read.maimages(files, source="imagene", columns=list(Rf="Signal >>Mean",Rb="Background Mean",Gf="Signal Mean",Gb="Background mean")) Matt, That's not quite right. You need RG<-read.maimages(files, source="imagene", columns=list(f="Signal Mean",b="Background Mean")) As the help says: columns: list with fields 'Rf', 'Gf', 'Rb' and 'Gb' giving the column names to be used for red and green foreground and background or, in the case of Imagene data, a list with fields 'f' and 'b'. This argument is not usually specified by the user but, if it is, it over-rides 'source'. Can I leave you to correct it on the list? Cheers Gordon >Best wishes, > >Matt Ritchie > >> >>please somebody help me out! >>sorry if once again I bother You with my basic questions... >>Thanks in advance. >> >>Emanuele
ADD COMMENT
0
Entering edit mode
Hi, I am trying to understand the affy package and more specially the rma function. I type : > data<-ReadAffy() > toto<-rma(data,subset=NULL,verbose=TRUE,destructive=TRUE,normalize=T RUE,backgrounbackground=TRUE,bgversion=1) and I've got as result : Note: You did not specify a download type. Using a default value of: Win32 This will be fine for almost all users [1] "Attempting to download mgu74av2cdf from http://www.bioconductor.org/data/cdfenvs/repos/" [1] "Download complete." [1] "Installing mgu74av2cdf" Note: Running R version 1.8.1 and package mgu74av2cdf was built for R version 1.8.0 , installing anyway. [1] "Installation complete" Background correcting Normalizing Calculating Expression How should I decide which download type I have to specify? What are the differences between all of these "cdf-types" ? Could you help me? Thank you.
ADD REPLY

Login before adding your answer.

Traffic: 833 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6