[BioC] Order in which ReadAffy() and read.affybatch()
ramasamy at cancer.org.uk
Fri Mar 18 20:04:55 CET 2005
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
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
> 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:
> file.names<-c("1.CEL", "2.CEL", "3.CEL", "4.CEL",
> "5.CEL","6.CEL","7.CEL", "8.CEL", "9.CEL",
Why not just do ReadAffy() ? It will return the filenames as column
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.
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