Error in processing xcell analysis about xcell HOT 7 CLOSED

[1] "Num. of genes: 0"

This means that the rownames in your data are not gene symbols. xCell assumes that you are using gene symbols and not some other gene ids.

Best,
Dvir

from xcell.

Thank for your reply!
According to your prompt, I rechecked the column of gene symbols (rownames) and confirmed that they indeed represent genes. However, it includes pseudogenes and mitochondrial genes, etc. It may be a problem.
Additionally, I attempted to integrate the gene expression data into another dataset and found that it can be analyzed normally, which confuses me. The data I am analyzing has undergone log2 transformation and limma differential analysis. I am not sure if this has an impact, or if I should analyze the original data.
I've uploaded the gene expression matrix file. If you could spare a moment to see where something might have gone wrong, I'd be very grateful!
Yours,
Tj
GSE77167_norm_exp_data.txt

from xcell.

The same problem also occurs here, only endured background correction, rma normalizaion and gene expression index calculation of probe intensities.
Really want to konw the cause and the solution, pls QAQ
Sorry for my disturbance.
GSE122626_norm_exp_data.txt

from xcell.

For some reason you have an extra space in all the gene names. rownames(a) = gsub(' ','',rownames(a)) should fix that...

from xcell.

Apologize for my silence for weeks, and thank for your reply from the bottom of my heart!
However, there's another issue emerged:

• xcell<-xCellAnalysis(GSE75050.norm, rnaseq=F)
• [1] "Num. of genes: 10514"
• Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

The same data can be analysied in the web xcell, so i wonder what's wrong and how can i figure it out. (i have updated all packages and changed network enviroment)
Thanks again!
Yours,
Tj

from xcell.

It's an issue with the matrixStats package. It made havoc throughout many packages. You need to upgrade your BioConductor and all associated with packages.

Best,
Dvir

from xcell.

I conquer it! tooooooooooo much appreciation for you!!!
Wish you a wonderful 2024! :)
Yours,
Tj

from xcell.