Hi Laura,

That's odd. I pretty much ran the same query on a list without issue. The output shows what records got deleted when I run it:

=========
> deldata2 <- labkey.deleteRows(
+ baseUrl="https://www.labkey.org",
+ folderPath="/Support Tickets/Dashboards/JonY",
+ schemaName="lists",
+ queryName="ListTest",
+ toDelete=data.frame(Key=c(2,3,4), stringsAsFactors=FALSE)
+ )
> deldata2
$rowsAffected
[1] 3

$queryName
[1] "ListTest"

$schemaName
[1] "lists"

$containerPath
[1] "/Support Tickets/Dashboards/JonY"

$rows
$rows[[1]]
$rows[[1]]$EntityId
[1] "0ac6dd24-bca7-1032-80ef-e5ac46246e24"

$rows[[1]]$Check
[1] FALSE

$rows[[1]]$Key
[1] 2

$rows[[1]]$Name
[1] "Frank"


$rows[[2]]
$rows[[2]]$EntityId
[1] "f5af4afa-bf8a-1032-80ef-e5ac46246e24"

$rows[[2]]$Check
[1] TRUE

$rows[[2]]$Key
[1] 3


$rows[[3]]
$rows[[3]]$EntityId
[1] "26e52ba1-d663-1032-b44e-e5ac46241b3e"

$rows[[3]]$Check
[1] FALSE

$rows[[3]]$Key
[1] 4


$command
[1] "delete"
>
=======

So that $rows section of yours should show the actual records being deleted rather than list().

Is that Peptide field the Primary Key for your list?

Regards,

Jon