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Question: DiffBind different read counts depending on dba.count scores specified
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gravatar for Lauma R
3 months ago by
Lauma R0
Cambridge
Lauma R0 wrote:

After closer inspection I noticed that Reads and RPKM values for the same samples in dba.counts$peaks changes depending which score metric I use. I was not quite sure if it something that should be expected, If that is the case, than why?

My code is:

dba.count_NON_INF.Reads <- dba.count( peak.test.NONINF, peaks= GRanges_NonINF, bRemoveDuplicates = FALSE, score = DBA_SCORE_READS )

dba.count_NON_INF.Reads$peaks
[[1]]
             
 
 
 
Chr     Start       End Score         RPKM Reads cRPKM cReads
1chr1     10014     10397    14   11.2965190    14     1      1
2chr1    180723    180910     6    9.9157375     6     1      1
3chr1    181437    181568     2    4.7181753     2     1      1
4chr1    629102    629953  2930 1064.0289316  2930     1      1
5 chr1    633374    634042  3603 1666.8755497  3603     1      1
6chr1    778350    778907    72   39.9477826    72     1      1
7chr1    827085    827736    30   14.2414970    30     1      1
8chr1    869749    870148    13   10.0689882    13     1      1
 
 
 
 
 
 
 
 
 
 
dba.count_NON_INF.RPKM <- dba.count(peak.test.NONINF, peaks= GRanges_NonINF, bRemoveDuplicates = FALSE, score = DBA_SCORE_RPKM )

dba.count_NON_INF.RPKM$peaks
[[1]]
               
 
 

 
Chr     Start       End        Score         RPKM Reads cRPKM cReads
1chr1     10014     10397   11.2965190   11.2965190    14     1      1
2chr1    180723    180910    8.2631146    8.2631146     5     1      1
3chr1    181437    181568    7.0772630    7.0772630     3     1      1
4chr1    629102    629953 1147.5533870 1147.5533870  3160     1      1
5chr1    633374    634042 1848.2286486 1848.2286486  3995     1      1
6chr1    778350    778907   40.5026129   40.5026129    73     1      1
7chr1    827085    827736   15.6656467   15.6656467    33     1      1
8chr1    869749    870148   10.0689882   10.0689882    13     1      1
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

 

Kind Regards 

Lauma 

ADD COMMENTlink modified 3 months ago • written 3 months ago by Lauma R0
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