[BioC] edgeR question
chunlai at umich.edu
chunlai at umich.edu
Mon Jul 5 18:54:38 CEST 2010
1. If I enter source("http://bioconductor.org/biocLite.R")
biocLite("edgeR") in R package,
Does the R package automatically install the latest version, which I
believe is 1.6.9?
2. While using readDGE function, there are sub-function in the guide like
(targets, skip=5,
comment.char="#").
What does it mean by skip=5 and comment.char="#" ?
If I don't type skip=5 or type something else like skip=10, the count
libraries sizes and counts
reported differently
So I wonder if this "skip" function makes any difference?
3. Again, using d<-readDGE(targets, skip=5, comment.char="#") function, the
result of $counts
showed incorrect read counts from the original txt. file
Is this a bug?
For example:
3MO1 3MO2 3MO3 18MO1
18MO2 18MO3
miR-192/CTGACCTATGAATTGACAGC 192720.6 23615.286 5085.223 0.0
0.000 0.000
However, the 18MO1, 18MO2, and 18MO3 do have reads for
miR-192/CTGACCTATGAATTGACAGC in the original txt. file
4. Since I have tags have very few read counts, I filter them out by
d<-d[rowSums(d$counts) > 1000,]
I wonder if edgeR compare tags which exist in one sample but are
filtered out in another sample?
For example:
3MO1 3MO2 3MO3 18MO1
18MO2 18MO3
miR-192/CTGACCTATGAATTGACAGC exist exist exist filter out
filter out filter out
3MO1, 3MO2 and 3MO3 are in one group, and 18MO1, 18MO2 and 18MO3 are in
another group
I want to compare the reads expression difference in these two groups
Does edgeR treat the 18MO1, 18MO2 or 18MO3 as 0 count and compare between
3MO and 18MO? or edgeR does not compare between them?
Another example:
3MO1 3MO2 3MO3 18MO1
18MO2 18MO3
miR-192/CTGACCTATGAATTGACAGC exist filter out exist filter out
filter out exist
Does edgeR compare reads between 3MO and 18MO groups?
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