Open beginner984 opened 2 years ago
Quick question. Did you run the "filter_counts" function on your data first? Is it possible you have genes in your data that are entirely zero?
Quick question. Did you run the "filter_counts" function on your data first? Is it possible you have genes in your data that are entirely zero?
Thank you
I have tried filtering now but the sane error
> clean_expr_data <- filter_counts(a)
Filtering user input
Genes and cells have been filtered, ready for estimating parameters
> dim(clean_expr_data)
[1] 3468 25038
>
After filtering 10000 genes were removed but the same error
> power_hierarchicell(data_summaries, n_genes = 100, n_per_group = 10)
Error in glm.fit(x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, :
NA/NaN/Inf in 'x'
>
Please, do you have any suggestion?
Thank you so much
Based on the number of genes that were dropped with "gene_thresh=0" there is likely a lot of zero inflation in the data. What happens if you move the "gene_thresh" to 1 or 2? Might be worth using the cell_thresh too, but I imagine if these are already processed data you have removed low quality cells.
If this problem persists, I might ask that you email me (kdzimmer@wakehealth.edu) your data (post-filtering to reduce size) and I will try and troubleshoot for you.
Hello
I have raw read counts of 3468 single cells from monocytes (I have already annotated my cell cluster). I extracted raw read counts from my Seurat data.
So this is how my data look like
I tried your software but I get error
I should mention I had two cancer patients "PN0252_0005" "PN0252_0008" and four controls
Do you know how I can solve this error please?
Thanks in advance