Different outputs of computeMatrix depending on binsize

I'd like to output a figure in +/-1kb around a center using computeMatrix as following command:

computeMatrix reference-point -S data.bw -R centers.bed -a 1000 -b 1000 -bs=10 -out newdata10.gz --referencePoint center


The bed file is like:

chr1 100 101


If I change -bs=1, two outputs of the same input newdata10.gz are quite different. Which's correct with my commands? Maybe I don't understand the meaning of binsize option.

As I mentioned on the list, what you're likely being surprised by is that computeMatrix is not summing values, but taking the average in each bin. You can change this with the --averageTypeBins option (the default is mean, you presumably want sum).
Update: For those wondering the cause of the confusion was due to not using --missingDataAsZero. In other words, including or not including NAs will lead to different results, since different numbers of values will be included.
• The default is mean, so unless you change it that's what you're getting. Feb 6 '18 at 17:56