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XZouProjects / scCODE

The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data
MIT License
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Can scCODE provide a complete list of DEgens? #5

Open Siteng999 opened 1 year ago

Siteng999 commented 1 year ago

Dear XZouProjects Thank you for providing such convenient DE analysis software! I have an inquiry for you about the details of the results. Can I get the full list of differential genes, including their fold changes and FDR values？ Gratefully

jawz-fd commented 1 year ago

Hello, the De_results of scCODE is the full list of the DE gene results obtained by the top_optimal methods. For example, the demo code：

run scCODE demo

library(scCODE)

demo data

data1<-data1_sccode

data2<-data2_sccode

"light", True or False, default as True, run scCODE in a light version which saves time. "top_ranked", the number of top-ranked strategies selected (5-10), default as 5

results

results<-scCODE(data1,data2,light = TRUE,top_ranked=5)

sccode_deresults

I think the "results$DE_results$P_adjust" and "results$DE_results$logFC" are what you wanted, P_adjust is the fdr_corrected Pvalue.

Siteng999 commented 1 year ago

Hi,jawz-fd

Thank you for your reply. I may not have phrased my query clearly. I found that the domain value of the final result is FDR<0.05. I was wondering if you could provide the p-value option and the list of all DE genes.

jawz-fd commented 1 year ago

Hi, I understand now. The scCODE program focus integrating the DE genes from sevel methods selected. Scince the program optionally takes a step of filtering gene before DE gene detection, some genes might be excluded from the final results. Your inquiry is meaningful, I would provide the information of all the genes applied by wilcox rank_sum test as reference. The package should be updated in several days.

Siteng999 commented 1 year ago

I really appreciate it！

XZouProjects commented 1 year ago

Hi, the package has been updated as v.1.2.0.2, the results on all genes applied by wilcox-test have been attached as results$results_wilcox.

Siteng999 commented 1 year ago

Hi，XZouProjects

The results in scCODE$results_wilcox seem to provide a list of only 5000 genes. The names of the remaining genes are NA.

I have attached my results file. 0606_test_results_wilcox.csv

XZouProjects commented 1 year ago

Hi, Thank you for pointing it out, we have fixed it now. Please retry and let us know if any problem appears.