17 Dec 2010, 13h10

> source(file="/projects/remc_bigdata/Karsan/R/20101217/bammap2counts_DE-H4ac.20101217.R")
[1] "some parameter settings"
fixed bins: 1000 bp; fragSize: 200 bp 
[1] "read in .bam files, filter reads"
Error in w$rname : $ operator is invalid for atomic vectors
> source(file="/projects/remc_bigdata/Karsan/R/20101217/bammap2counts_DE-H4ac.20101217.R")
[1] "some parameter settings"
fixed bins: 1000 bp; fragSize: 200 bp 
[1] "read in .bam files, filter reads"
/projects/remc_bigdata/Karsan/HS1238_kd/maq2sam/HS1238.h.sorted.bam : Read 16316102 mapped non-dup. reads, 88.74 percent with MAPQ>10
/projects/remc_bigdata/Karsan/HS1235_ctl/maq2sam/HS1235.h.sorted.bam : Read 21753664 mapped non-dup. reads, 90.46 percent with MAPQ>10
/projects/analysis/analysis5/HS1238/62P7NAAXX_2/bwa/62P7NAAXX_2.bam : Read 35023769 mapped non-dup. reads, 92.59 percent with MAPQ>10
/projects/analysis/analysis5/HS1235/62P7NAAXX_1/bwa/62P7NAAXX_1.bam : Read 34280727 mapped non-dup. reads, 92.29 percent with MAPQ>10
[1] "create table of windows along the genome"
[1] "create count table after extending reads to be length fragSize"
Counting in HS1238_kd 
Counting in HS1235_ctl 
Counting in HS1238_kd_2 
Counting in HS1235_ctl_2 
Counting successful.
[1] "filter on the total count for a bin (10)"
[1] "Get normalizing factors for edgeR."

 process as replicates 
d.rep$common.dispersion= 0.06038636 
[1] "exactTest()"
Comparison of groups:  HS1238_kd - HS1235_ctl 
[1] "write.table, all records, regardless of p-val"

 process as separate old and new run pairs 
[1] "estimate common dispersion"
1000 bp bins: d.sep$common.dispersion= 1e-16 
[1] "old pair: exactTest()"
Comparison of groups:  HS1238_kd - HS1235_ctl 
[1] "write.table, all records, regardless of p-val"
[1] "new pair: exactTest()"
Comparison of groups:  HS1238_kd_2 - HS1235_ctl_2 
[1] "write.table, all records, regardless of p-val"
[1] "Now compare the old KD/ctl to the new KD/ctl pair"
[1] "compare p-values / log-fold changes"
[1] "Use Z-scores"
[1] "write out PDF"
[1] "Alternative for comparing tech replicates: a simple pairs() plot"
Warning message:
In estimateCommonDisp(d.sep) :
  There is no replication.  Setting common dispersion to 0.