Recent changes to Bioconductor packages

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madman@jimmy.harvard.edu ▴ 850

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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

SAGE annotate geneplotter graph SAGElyzer Rdbi SAGE annotate geneplotter graph SAGElyzer • 1.3k views

ADD COMMENT • link 21.9 years ago • updated 21.8 years ago madman@jimmy.harvard.edu ▴ 850

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madman@jimmy.harvard.edu ▴ 850

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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 COMMENT • link 21.9 years ago madman@jimmy.harvard.edu ▴ 850

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madman@jimmy.harvard.edu ▴ 850

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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 COMMENT • link 21.9 years ago madman@jimmy.harvard.edu ▴ 850

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madman@jimmy.harvard.edu ▴ 850

@madmanjimmyharvardedu-174

Last seen 10.3 years ago

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 COMMENT • link 21.8 years ago madman@jimmy.harvard.edu ▴ 850

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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 REPLY • link 21.8 years ago Hinnerk Boriss ▴ 220

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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 REPLY • link 21.8 years ago Jean Yee Hwa Yang ▴ 920

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