Results form R are different respect online website about xcell HOT 6 OPEN

The online version uses rounding. You can try it your self -

scores = round(scores*1000)/1000

P-values are an attempt to assess whether the scores are significantly different than zero. If the p-values are high (>0.2) it means that the presence of this cell type in the mixture is low. I should note that providing confidence here is tough, so I won't make much of it.

Best,
Dvir

from xcell.

I round it as you say but the results are still different. My passages are:

devtools::install_github('dviraran/xCell',force = TRUE)
library(xCell)
xcell_r <- xCellAnalysis(d0)
xcell_r = round(xcell_r*1000)/1000

am i doing something wrong? do you think thant is better the version online or on R?

from xcell.

I used the same matrix for both the analysis, and on the online website i condiser N=64 and I click on the RNA-seq bottom because my matrix is a bulk RNA-seq. My matrix looks like this

( the data are on excel so they have a , but when I upload the file on the website I use a txt file)

from xcell.

Hi Michela,

I can't guess what is the issue, but you sent me the data and I can see from it that there are differences in the names of the samples and the order, so my intuition is that you are not using the same TPM matrix for both analyses. Beyond that I can't tell you what is going on. I tried myself one dataset and there where no differences.

I strongly recommend using the R version, with limited cell types which are relevant for your cell types.

https://link.springer.com/protocol/10.1007/978-1-0716-0327-7_19

Best,
Dvir

from xcell.

from xcell.

from xcell.