[BioC] Order in which ReadAffy() and read.affybatch()

[Hrishikesh Deshmukh]

Hi All,

I am not that familiar with BioC terms, i know
readaffy() and read.affybatch() makes it easy to read
CEL file and two "different" kinds of objects are
created and typically some "kinds" of analyses for
example boxplot() may work with readaffy() and not
with read.affybatch() and hist() might work well with
read.affybatch()!! But these are the kinds of
questions for which docs are non-existant! Vignettes
help but they only whet your appetite but do not
satisfy your hunger!! Sorry went in different
direction.

I do work with multiple OS and thanks for the piece of
very important information. One simple way to make
sure no matter what order the files are read, doing
simple hist() and/or boxplot() and then making sure
that right labels(filenames) are given for the
lines/plots.....now to do this simple thing one has to
go through lot of documentation! Ahhh!!!

Is there a book on BioC specifically which will help
people be conversant with terms and use it
efficiently!!! 

But hats off to the mailing list members for answering
my simple/naive questions.

Regards,
Hrishi


--- Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
wrote:
> See comments below.
> 
> On Fri, 2005-03-18 at 08:26 -0800, Hrishikesh
> Deshmukh wrote:
> > Hello All,
> > 
> > I have questions about the order in which
> ReadAffy()
> > and read.affybatch() reads in affy CEL files. I
> need
> 
> Alphabetically, but the behaviour may vary between
> Windows and Linux due
> to case sensitivity.
> 
> > this piece of information because i want to label
> the
> > arrays when i look at hist() and boxplot(). I want
> to
> 
> This is a dangerous practice as you will be assuming
> that filenames are
> read alphabetically. If you work on multiple OS,
> this might be a
> nightmare.
> 
> Besides, since the filenames are used as the column
> names in ReadAffy
> you do not need to need to care about which order it
> reads in the files.
> 
> raw <- ReadAffy()
> head( exprs( raw ) )
> 
>        a.CEL    b.CEL    c.CEL   d.CEL
> [1,]    253.8    335.8    176.5   238.3
> [2,]  19607.3  19437.5  11239.5 20985.5
> [3,]    218.0    275.3    169.5   263.5
> [4,]  20284.5  19956.8  11324.8 21180.5
> [5,]     87.5     94.8    100.3    78.5
> [6,]    224.5    237.8    186.5   165.8
> 
> Then you can do a strsplit() the column names or
> match() it to something
> else.
> 
> 
> > make sure that right labels (filenames) are
> displayed
> > for its corresponding lines/boxplots. 
> > 
> > Is there a book specifically on BioC, this would
> be a
> > big help?
> > 
> > In general on what basis does one accept/reject
> arrays
> > from a pool of replicates! The hist() and
> boxplot()
> > shows clearly that all the arrays (replicates) do
> not
> > show the same "behaviour".
> 
> This is before preprocessing right ? There could be
> systematic noises
> that preprocessing algorithms can handle. I think
> people usually reject
> on the basis of biological evidence such as
> housekeeping genes, RNA
> degradation plots or eye-balling the chip. 
> 
> 
> > Here are the code fragments:
> > library(affy)
> > library(hgu95av2cdf)
> > library(hgu95av2probe)
> > library(matchprobes)
> > data(hgu95av2probe)
> > summary(hgu95av2probe)
> > file.names<-c("1.CEL",  "2.CEL",  "3.CEL", 
> "4.CEL", 
> > "5.CEL","6.CEL","7.CEL",  "8.CEL",  "9.CEL", 
> > "10.CEL", 
> >
>
"11.CEL","12.CEL","13.CEL",14.CEL","15.CEL","16.CEL","17.CEL")
> > M<-read.affybatch(filenames=file.names,
> > description=NULL,notes="",compress=F,   
> > m.mask=F,rm.outliers=F,rm.extra=F,verbose=T)
> 
> Why not just do ReadAffy() ? It will return the
> filenames as column
> names. 
> 
> > hist(M)
> > legend(12,1.2,sampleNames(M),col=1:17,lty=1:17) 
> 
> Interesting. Why do I get a density plot when I call
> hist() on an
> Affybatch class ?
> 
> > When i run the legend line i see hist() displays
> > different "lines" and legend does not match
> correctly!
> > 
> > Thanks in advance.
> > Hrishi
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>