Raw Intensity Extraction From A Snp_6 Affymetrixcelset

Question

[Jonathan Crowther]

Hi all,

I suppose this is a simple enough task even for a newbie like me, I have found a similar related post but I have two questions:

My First Question when I use the following commands in R:

library(aroma.affymetrix)

cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") 
cs <- AffymetrixCelSet$byName("Arles", cdf=cdf)

unit <- indexOf(cdf, "SNP_A-8656720")
y <- readUnits(cs, units=unit)
str(y)

This allows me to gather the raw intensities for a SNP or CN probe. as follows:

$`SNP_A-8656720`$A$intensities
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,]  786  807 1051  879 1971 1447 1826  236 1249  2335  1140   416  1147  2054
[2,]  694  823 1027  835 1673 1167 1729  252 1068  2339   982   411   769  1786
[3,]  752  665  913  820 1621 1356 1555  248 1344  2362  1417   339   991  1835


$`SNP_A-8656720`$G
$`SNP_A-8656720`$G$intensities
     [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,]  273 1014  481 1012  402  383  421 1138  321   861   614  1859   687   549
[2,]  222  528  476  825  602  719  460  912  417   796   650  1617   537   661
[3,]  259  781  543  754  492  452  550  909  316   743   518  1847   529   651

From the previous post this data is supposed to reference to the A and B allele and for the forward and reverse strands. My question is, what refers the Allele A/B ($A/$G) and forward / reverse, also by that logic there should be 4 sets of data? As for CN probes this is much more obvious as there is only one probe interrogating the position.

My Second Question is in relation to expanding this code in order to generate the raw intensities of all the SNP_ probes and then to run the Sam e for CN_ probes so that I have the raw intensities for each seperately?

Cheers,

Jonathan

Answer 1

[Jonathan Crowther]

To answer the second Question it is possible to extract the SNP or CN probes by entering a pattern instead of a single probe so in the case of SNP or CN:

SNP Probes:

unit <- indexOf(cdf, "SNP_A-")

CN Probes:

unit <- indexOf(cdf, "CN_")

Doing this will creates a file for all the probes with that pattern.

Answer 2

[David Quigley]

On that platform (and the others that I am familiar with) any given SNP is interrogated either on the forward or the reverse allele, but not both. That's why there are two numbers (A and B intensity) and not four for a given locus, and it's why you have to track for each SNP whether the forward or reverse strand is being interrogated. I think the fact that Affymetrix may have designed probes to query both strands, but only uses one of the strands for each SNP, may be confusing the issue.

Answer 3

[Jonathan Crowther]

Hi David,

Thank you for your reply, I agree about the A and B allele indicating the $A and $G however in as far as I have read before from H Bengtsson, that this is the case of forward and reverse strands:

https://groups.google.com/forum/?fromgroups=#!searchin/aroma-affymetrix/Raw$20intensities/aroma-affymetrix/cHqCjBFw-wQ/ajItYU91OgAJ