Question: Recent changes to Bioconductor packages
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gravatar for madman@jimmy.harvard.edu
16.7 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the files madman/Rpacks/NEWS and NEWS.old at any time for up to date information. Also, please remember to edit the NEWS file yourself after making any noteworthy changes to the packages - follow the format used in these files and make sure to sign your name to the entry. ---------------------------------------------------------------------- - Jan 31, 2003: dbTools - a new package added to handle basic database queries for Rdbi and RODBC. - JZ Jan 31, 2003: SAGElyzer - functions added for setting up a database for sage libraries and finding sage tags with similar expression patterns to a given target sage tag. - JZ Jan 30, 2003: annotate, added a function to build UniGene queries. These are more common for cDNA arrays. RG Jan25/2003 Added lots of stuff to the graph class. New generalGraph class, hash tables, and a variety of other helpers - RG Jan 25/2003 Added T. Lumley's color ramp functions to geneplotter - RG
ADD COMMENTlink modified 16.7 years ago • written 16.7 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
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gravatar for madman@jimmy.harvard.edu
16.7 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - Feb 07, 2003: SAGElyzer - merging SAGE libraries, writing data to DB, and finging tags with a similar expression pattern as a target tag tested for Unix and partically tested for windows - JZ Feb 05, 2003: Ruuid - Win32 functionality was added to this package - JG Feb 05, 2003: edd: proper vignette header items added VJC
ADD COMMENTlink written 16.7 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
0
gravatar for madman@jimmy.harvard.edu
16.7 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - Feb. 14, 2003: Data packages: XML data files for human and mouse updated. R data packages will be available soon - JZ Feb 13, 2003: getBioC: Added option getAllDeps (see following note) -JG Feb 13, 2003: reposTools: new option to install and update.packages2, getAllDeps=FALSE, if set to TRUE, will not prompt the user to download dependencies, but get the automatically. -JG Feb 08, 2003: affy: vignette to outline how to get CEL data from other sources than the current '.CEL' files -- LG
ADD COMMENTlink written 16.7 years ago by madman@jimmy.harvard.edu850
Answer: Recent changes to Bioconductor packages
0
gravatar for madman@jimmy.harvard.edu
16.7 years ago by
madman@jimmy.harvard.edu850 wrote:
This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history. ---------------------------------------------------------------------- - Feb. 20, 2003: Data package hgu133b added. - JZ Feb 19, 2003: Data packages updated and mug74b, mgu74c, rgu34b, rgu34c added - JZ Feb 17, 2003: exprDB: Now supports esApply via a masking function in exprDB. esApply now transparently employs both exprSets and exprDBs. - BE Feb 16, 2003: exprDB: using S4 classes and implementing a fair amount of exprSet support. Also added "apply," which has remarkably good performance characteristics compared to esApply. - BE
ADD COMMENTlink written 16.7 years ago by madman@jimmy.harvard.edu850
Hi, I am trying to construct an object of class marrayRaw from scratch. I have red and green intensities stored in data frames that look something like this: G_name chip1 chip2 ... chipN Gene1 0.1 2. 3. . . . GeneM 2. 4. 5. Then I tried the following: > infos <- new("marrayInfo", maLabels=dimnames(green)[[1]]) > exp2raw <- new("marrayRaw", maRf=matrix(red), maGf=matrix(green), maTargets=infos) Now looking at the object reveals that something went wrong: (btw: I was having 10 chips) > exp2raw Pre-normalization intensity data: Object of class marrayRaw. Number of arrays: 1 arrays. A) Layout of spots on the array: Array layout: Object of class marrayLayout. Total number of spots: Dimensions of grid matrix: rows by cols Dimensions of spot matrices: rows by cols Currently working with a subset of spots. Control spots: Notes on layout: B) Samples hybridized to the array: Object of class marrayInfo. [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "K" ... Number of labels: 348 Dimensions of maInfo matrix: rows by columns Notes: C) Summary statistics for log-ratio distribution: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's [1,] NA NA NA NA NA NA 10 D) Notes on intensity data: ---------- What am I missing here. There is apparently only one chip recognized, even though I supplied a matrix with 10 columns. Do I need to specify a layout? Right now I don't really care about spacial effects, that's why I didn't bother playing with it. I hope you can help me to bring me on the right track. Cheers, Hinnerk
ADD REPLYlink written 16.7 years ago by Hinnerk Boriss220
Hi Hinnerk, It is likely that matrix(red) isn't a M by N matrix. Check dim(matrix(red)) class(matrix(red)) In addition, try the following: exp2raw <- new("marrayRaw", maRf=as.matrix(red), maGf=as.matrix(green)) exp2raw To get a matrix of log-ratios, use maM(exp2raw) Hope this helps Jean > GeneM 2. 4. 5. > > Then I tried the following: > > > infos <- new("marrayInfo", maLabels=dimnames(green)[[1]]) > > exp2raw <- new("marrayRaw", maRf=matrix(red), maGf=matrix(green), > maTargets=infos) > > Now looking at the object reveals that something went wrong: (btw: I was > having 10 chips) > > > exp2raw > Pre-normalization intensity data: Object of class marrayRaw. > > Number of arrays: 1 arrays. > > A) Layout of spots on the array: > Array layout: Object of class marrayLayout. > > Total number of spots: > Dimensions of grid matrix: rows by cols > Dimensions of spot matrices: rows by cols > > Currently working with a subset of spots. > > Control spots: > > > Notes on layout: > > > B) Samples hybridized to the array: > Object of class marrayInfo. > > [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "K" > ... > > Number of labels: 348 > Dimensions of maInfo matrix: rows by columns > > Notes: > > > C) Summary statistics for log-ratio distribution: > Min. 1st Qu. Median Mean 3rd Qu. Max. NA's > [1,] NA NA NA NA NA NA 10 > > D) Notes on intensity data: > > ---------- > What am I missing here. There is apparently only one chip recognized, > even though I supplied a matrix with 10 columns. Do I need to specify a > layout? Right now I don't really care about spacial effects, that's why > I didn't bother playing with it. I hope you can help me to bring me on > the right track. > > Cheers, > Hinnerk > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLYlink written 16.7 years ago by Jean Yee Hwa Yang920
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