Thread: DESeq problems
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Old 08-05-2013, 04:48 AM   #13
vd4mindia
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Location: Milan

Join Date: May 2013
Posts: 40
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Sorry I am trying to start a new thread but am unable to do that , I donot know why.. yes I am converting the values to integer as with the direct raw counts I cannot run the DESeq commands as they are not integer values. So I have to convert them to the nearest integer and then carry out the analysis.

gene PGT-1 PGT-0 PGT-2 PDGT-0 PDGT-1
XLOC_000001 2603 1534 1764 9030 4309
XLOC_000002 304 175 208 1095 835
XLOC_000003 195 80 109 687 454
XLOC_000004 66 49 54 236 90
XLOC_000092 365 211 242 1523 624
XLOC_000093 0.666667 0.5 1 1.66667 3.33333
XLOC_000094 0 0 0 0 0
XLOC_000095 6 11.4802 4.56786 8.49762 7.22143
XLOC_000096 0 0.25 0 0 0
XLOC_000097 195.561 90.88 114.348 262.98 246.68
XLOC_000098 0 7.79035 3.89757 0 1.30276
XLOC_000099 39 18 23 55 27
XLOC_000100 10.9163 5 3 12.8974 8
XLOC_000101 533 32 28 854 288
XLOC_000102 2756.33 3090.17 2311 4873 1677.25


You can see the raw counts are having decimal values which does not work for DESeq so I converted them to nearest integer.
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