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?

My name is Jennifer Lai, a PhD student in Univeristy of Michigan I have some questions about edgeR 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? Thanks