Different results between online analysis and R software

[YKH810325]

Dear all,
I face a problem that reveals the different results between online server and R software.

The results of online servser:

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	X868N	X879N	X888N	X1268N	X868K	X879K	X888K	X1268K	X1866_1
aDC	382.8578	40.43974	178.9125	742.0114	1394.624	1230.12	1115.967	1867.441	52.3757
Adipocytes	2247.73	1700.62	629.2453	1800.12	0	838.5027	216.2571	570.4954	2044.795
Astrocytes	534.5511	126.4531	445.6113	347.6849	979.0361	589.6684	382.6429	596.2315	688.1574
Basophils	700.9111	627.7844	382.2197	484.5543	609.3579	626.2382	350.6588	234.7838	479.8278
B-cells	151.546	74.85261	102.2584	167.2138	651.2887	228.27	413.6087	1184.226	41.58247

The results of R software (I perform "xCellAnalysis" function.):

<style> </style>

	X868N	X879N	X888N	X1268N	X868K	X879K	X888K	X1268K	X1866_1
aDC	4.63E-21	1.67E-18	4.64E-21	0.019692	0.110267	0.075325	0.051219	0.18708	0
Adipocytes	0.02524	0.010217	0	0.010961	0	2.24E-21	0	0	0.014607
Astrocytes	0	0	0	0	2.11E-18	0	3.24E-18	0	6.11E-20
Basophils	0.090306	0.075668	0.017097	0.0248	0.043113	0.060791	0.009643	5.25E-18	0.029714
B-cells	0	1.18E-19	2.15E-20	3.12E-18	1.16E-18	1.36E-18	0.008258	0.079919	0

Why are they different?
How can I get similiar results in R software?

[dviraran]

Hi,

The first table is the raw scores (first link in the email you received), while the second table is the final xCell scores. We recommend using the final scores. You can extract the raw scores from the package using just the rawEnrichmentAnalysis function.

Best,
Dvir

[YKH810325]

Got it.

When I perform "rawEnrichmentAnalysis(a, genes = rownames(a))", I get another error "argument "signatures" is missing, with no default ".

[dviraran]

Should be something like this:

raw.scores = rawEnrichmentAnalysis(as.matrix(expr),
  xCell.data$signatures,
  xCell.data$genes)

You can find this, and other examples, in this paper: https://link.springer.com/protocol/10.1007/978-1-0716-0327-7_19