[BioC] Affy CEL file herder info

[Henrik Bengtsson]

AFFXPARSER:
There is readCcgHeader() that allows you to access the header of such
CEL files too (please note that this function is a working beta that
does not utilize Fusion SDK, but was coded up for internal test
reasons).

AROMA.AFFYMETRIX:
Alternatively, you can use the high-level API of aroma.affymetrix (on
CRAN) package to do this for you:

library("aroma.affymetrix");
dsR <- AffymetrixCelSet$byName("HapMap270,6.0,CEU,testSet",
chipType="GenomeWideSNP_6");
print(dsR);

AffymetrixCelSet:
Name: HapMap270
Tags: 6.0,CEU,testSet
Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6
Number of arrays: 6
Names: NA06985, NA06991, ..., NA07019
Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16
Total file size: 395.13MB
RAM: 0.01MB

pathnames <- getPathnames(dsR);
str(pathnames);
 Named chr [1:6] "C:/Users/hb/Documents/My Data/rawData/HapMap270,6.0,CEU,testSe
t/GenomeWideSNP_6/NA06985.CEL" ...
 - attr(*, "names")= chr [1:6] "NA06985" "NA06991" "NA06993" "NA06994" ...

ts <- getTimestamps(dsR);
print(ts);
[1] "2007-03-06 12:13:04 PST" "2007-03-06 16:15:53 PST"
[3] "2007-03-06 19:17:16 PST" "2007-03-06 17:05:24 PST"
[5] "2007-03-06 17:38:23 PST" "2007-03-06 15:12:49 PST"

str(ts);
 POSIXlt[1:9], format: "2007-03-06 12:13:04" "2007-03-06 16:15:53" ...

File by file:

df <- getFile(dsR, 2);
print(df);
AffymetrixCelFile:
Name: NA06991
Tags:
Full name: NA06991
Pathname: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6/NA06991.CEL
File size: 65.85 MB (69045921 bytes)
RAM: 0.01 MB
File format: v1 (binary; CC)
Platform: Affymetrix
Chip type: GenomeWideSNP_6
Timestamp: 2007-03-06 16:15:53

ts <- getTimestamp(df);
print(ts);
[1] "2007-03-06 16:15:53"
str(ts)
 POSIXlt[1:9], format: "2007-03-06 16:15:53"

/Henrik

On Wed, Jan 6, 2010 at 12:06 PM, He, Yiwen (NIH/CIT) [C]
<heyiwen at mail.nih.gov> wrote:
> Hi,
>
> We are trying to extract the header info in the affy CEL files, particularly the scan date and time and the scanner serial number. The affyxparser:readCelHeader and affyio:read.celfile.header function works fine for the text and binary CEL files. However when I tried them on the AGCC generated CEL files, the header slots are empty. Is there a way to obtain such info for the AGCC CEL files?
>
> Thank you very much!
>
> Yiwen He
> NIH/CIT/DCB/BIMAS
>
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