eblancoga
commented
6 months ago Hi Rafael,
Sure, I've seen sometimes this bug due to very low number of spike-in reads (or null) in the samples. What proportion/totals of human vs spike-in genome reads do you see in your BAM files?
Best,
Enrique
Dr. Enrique Blanco García (PhD)
https://sites.google.com/site/eblancog2014/
http://orcid.org/0000-0001-6261-7370
Epigenetic Events in Cancer (L. Di Croce's lab) Gene Regulation, Stem Cells and Cancer Centre for Genomic Regulation (CRG)
C/ Dr. Aiguader, 88
08003 Barcelona
Spain
De: Rafael @.> Enviado: martes, 16 de abril de 2024 10:28 Para: eblancoga/spikChIP @.> Cc: Subscribed @.***> Asunto: [eblancoga/spikChIP] normalize.loess error (Issue #5)
Hi,
Thank you for developing such a useful tool. I'm currently attempting to use spikChIP with human cell line samples and have encountered an error while running the R script (avg.R). The error message is:
mn <- normalize.loess(m,subset=s) Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : NA/NaN/Inf in foreign function call (arg 1) In addition: There were 44 warnings (use warnings() to see them)
I have verified that all values within the script are greater than 0.1 and there are no NAs.
Here is my R session:
sessionInfo() R version 4.0.3 (2020-10-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS
Matrix products: default
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base
other attached packages: [1] MASS_7.3-60.0.1 affy_1.68.0 Biobase_2.50.0 [4] BiocGenerics_0.36.1
loaded via a namespace (and not attached): [1] BiocManager_1.30.22 zlibbioc_1.36.0 compiler_4.0.3 [4] affyio_1.60.0 preprocessCore_1.52.1
Could you provide some guidance on resolving this issue? I appreciate your help.
Thanks
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rlbc
Hi,
Thank you for developing such a useful tool. I'm currently attempting to use spikChIP with human cell line samples and have encountered an error while running the R script (avg.R). The error message is:
All values within the script are greater than 0.1, and there are no NAs, at least.
Here is my R session:
Could you provide some guidance on resolving this issue? I appreciate your help.
Thanks