Mercurial > repos > fubar > differential_count_models
comparison rgedgeRpaired_nocamera.xml @ 123:51f998262ada draft
Uploaded
| author | fubar |
|---|---|
| date | Tue, 25 Nov 2014 05:36:47 -0500 |
| parents | 6ded550dcc7d |
| children | 731315bd6e48 |
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| 122:6ded550dcc7d | 123:51f998262ada |
|---|---|
| 544 | 544 |
| 545 | 545 |
| 546 DGLM = glmFit(myDGEList,design=mydesign) | 546 DGLM = glmFit(myDGEList,design=mydesign) |
| 547 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed | 547 DE = glmLRT(DGLM,coef=ncol(DGLM\$design)) # always last one - subject is first if needed |
| 548 efflib = myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors | 548 efflib = myDGEList\$samples\$lib.size*myDGEList\$samples\$norm.factors |
| 549 normData = (1e+06*myDGEList\$counts/efflib) | 549 normData = cpm(myDGEList) |
| 550 ### normData = (1e+06*myDGEList\$counts/efflib) | |
| 550 uoutput = cbind( | 551 uoutput = cbind( |
| 551 Name=as.character(rownames(myDGEList\$counts)), | 552 Name=as.character(rownames(myDGEList\$counts)), |
| 552 DE\$table, | 553 DE\$table, |
| 553 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), | 554 adj.p.value=p.adjust(DE\$table\$PValue, method=fdrtype), |
| 554 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData, | 555 Dispersion=myDGEList\$tagwise.dispersion,totreads=cmrowsums,normData, |