Comparison between Website and R Tool Results

[littleeun]

Hello

To make sure I ran xcell properly, I downloaded the sample expression file from the https://comphealth.ucsf.edu/app/xcell site and ran the website and r tool at the same time, but the cell type is different and the value is different. Are the websites and r tools separate? And are there any sample files and result files available for running the check?

Thank you.

[dviraran]

They use the same code. In the web tool there is rounding to the third decimal point for the enrichment scores, but other than that it's similar. There could be differences in the versions of the dependent packages which may lead to some differences.

--Dvir

[littleeun]

Thank you for your reply.

Are you saying to round the xcell result of rtool version?

library(xCell) result <- xCellAnalysis(unique_merge) result = round(result*1000)/1000

I added the code this way, but there is a difference in the value, am I doing it wrong?

Thank you.

[dviraran]

What kind of difference?

[littleeun]

sample.txt xCell_result_R.txt xCell_result_website_1546030124.txt

Here are the results obtained from the r tool and from the website. In this result file, for example, if you look at the results of Basophils of GSM565269, it can be seen that 0.003596682 websites are 0.0241 in the r tool. It was said that the difference was made by rounding up from the third decimal place, but I don't know if this result can be said to be the same, so I hope you check it.

Thank you.

[rtrelator]

Hi there! I also had this issue of different score values between web server and the xCellAnalysis wrapper function. I also noticed that when I set rnaseq=F in the wrapper, I get similar results from the webtool even if I checked RNAseq in the webtool. In addition, the results from the webtool are the same regardless if you check RNAseq box or not. Could you confirm if this was the same case as yours? @dviraran Could you confirm if this is indeed the case? Thank you.