Hello All,
I made a DGEList object.
d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$HGNC_symbol)
I added additional parameters to the list.
rownames(d) <- COUNTS$Ensembl d$ENTREZ <- COUNTS$NCBI_geneID d$ENSEMBL <- COUNTS$Ensembl d$Symbol <- COUNTS$HGNC_symbol d$length <- COUNTS$Length d$gc <- COUNTS$GC
Then I filtered the list.
keep <- rowSums(cpm(d)>2)>= 3 d <- d[keep,] dim(d)
13980 36
The filtering worked on the original DGEList object but not on the added parameters.
$genes
genes
ENSG00000000003 TSPAN6
ENSG00000000419 DPM1
ENSG00000000457 SCYL3
ENSG00000000460 C1orf112
ENSG00000001036 FUCA2
13980 more rows ...
$ENTREZ
[1] 7105 64102 8813 57147 55732
58228 more elements ...
$ENSEMBL
[1] ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ENSG00000000460
58233 Levels: ENSG00000000003 ENSG00000000005 ENSG00000000419 ENSG00000000457 ... ENSG00000284600
58228 more elements etc.
I was wondering if there is a way to filter the added parameters as well to keep all the info in one place for downstream analysis.
Thank you for your help and time.
Anita
It worked. Thanks.