Hi Ina:

    It surprised me that you only got around 320,000 beads. You should 
see at least 700,000 beads for each strip since there are about 24,000 
bead types in each strip and each bead type have 30 or more beads. And 
we actually saw about 1 million beads for each strip for our data. I 
suspect you did not retrieve bead level data correctly.

Cheers,
Wei

Ina Hoeschele wrote:
> I have a total of 319952 beads. So I printed the information for the 
> first 10 and for 10 others towards the end. Even for the first 10 beads 
> the GrnX and GrnY are not negative. Here it is.
>   
>>  BLData[[1]][1:10,]
>>     
>    ProbeID          G Gb      GrnX      GrnY
> 1    10008  0.0000000  0 1556.7592 13526.200
> 2    10008  2.5249867  0 1713.2862 17711.700
> 3    10008 -0.0359710  0   45.9317  6676.658
> 4    10008  0.0000000  0 1401.8142  2153.181
> 5    10008  0.0000000  0 2078.2252 15974.100
> 6    10008 -6.8111267  0 1193.8842  8654.250
> 7    10008  0.0000000  0   45.0026 13990.970
> 8    10008 77.2345222  0  542.1487 14834.780
> 9    10008 -0.8237067  0 1341.1462 13791.170
> 10   10008 -0.2324444  0 1312.7072  7549.003
>   
>>  BLData[[1]][300000:300010,]
>>     
>        ProbeID           G Gb      GrnX      GrnY
> 300000 2140131  0.00000000  0 1258.9752 17301.580
> 300001 2140131 -0.24859133  0  398.1137  6108.199
> 300002 2140131 -0.07388444  0 2094.6222 16298.300
> 300003 2140131  0.00000000  0  642.9227  2094.740
> 300004 2140131 11.67171933  0 1352.2322  6294.191
> 300005 2140131  0.00000000  0 1104.5312 14069.740
> 300006 2140131 -0.15372500  0  963.8952  9653.909
> 300007 2140131  0.00000000  0  161.5619 14317.910
> 300008 2140131 -0.08331556  0 1515.5492 13932.460
> 300009 2140131  0.61296444  0 1934.0542 15118.710
> 300010 2140131  0.00000000  0  177.0217 16717.080
>
>
>   

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