-
Notifications
You must be signed in to change notification settings - Fork 24
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 6435, 5148 #115
Comments
I'm also facing the same issue: [1] " raw data - genes: 24516 cells: 3246" |
I also am getting this error! `[1] " raw data - genes: 23686 cells: 7930" Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:
The following objects are masked from ‘package:base’:
Warning message: Loading required package: foreach Loading required package: iterators Loading required package: parallel [1] "found 30 confident non malignant cells"
|
Hello everyone,
Thanks @jakubotreba @naila53 @Ahmed-Ghobashi . Regards |
@AntonioDeFalco Thank you for your reply. 1.I did not reinstall SCEVAN. I will do it this week I will reinstall the package and will keep you posted. |
Hi @AntonioDeFalco ,
Both human and mouse organisms? |
to give you updates. After reinstalling the package, it worked but not on all the samples. Four samples were integrated using Seurat and processed the same way. Then I split them based on orgi.ident and 3 of my samples worked fine and one sample gave me the same error. |
Hi ! Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 7154, 6080
|
Thank you for developing this software.
I am trying to run on my samples, but I keep getting this error
Any help will be appreciated
[1] " raw data - genes: 23137 cells: 41453"
[1] "1) Filter: cells > 200 genes"
[1] "2) Filter: genes > 10% of cells"
[1] "7224 genes past filtering"
[1] "3) Annotations gene coordinates"
[1] "found 30 confident non malignant cells"
[1] "6842 genes annotated"
[1] "4) Filter: genes involved in the cell cycle"
[1] "6435 genes past filtering "
[1] "5) Filter: cells > 5genes per chromosome "
[1] "6) Log Freeman Turkey transformation"
[1] "A total of 41450 cells, 6435 genes after preprocessing"
[1] "7) Measuring baselines (confident normal cells)"
[1] "8) Smoothing data"
[1] "9) Segmentation (VegaMC)"
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 6435, 5148
In addition: Warning messages:
1: In asMethod(object) :
sparse->dense coercion: allocating vector of size 7.1 GiB
2: In asMethod(object) :
sparse->dense coercion: allocating vector of size 7.1 GiB
3: In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.1 GiB
4: In parallel::mclapply(1:ncol(count_mtx_relat), nonLinSmooth, mc.cores = par_cores) :
scheduled cores 6, 8, 10, 17 did not deliver results, all values of the jobs will be affected
5: In matrix(unlist(test.mc), ncol = ncol(count_mtx_relat), byrow = FALSE) :
data length [213378165] is not a sub-multiple or multiple of the number of rows [5148]
The text was updated successfully, but these errors were encountered: