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
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