User: rahel14350

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rahel1435020
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New User
Location:
United States
Last seen:
2 days, 5 hours ago
Joined:
3 years, 4 months ago
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r*********@gmail.com

Posts by rahel14350

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Comment: C: count tables from RNA-seq data on GEOmetadb
... Dear Sean, Many thanks for your prompt reply. I did also tried GEOquery but I need to do it per study (GSE*) and then I can use Limma. I can not get the table counts for all of the studies using getGEO(). I also can combine/merge two eset but when they are on the same platform or the number of sampl ...
written 6 weeks ago by rahel1435020
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count tables from RNA-seq data on GEOmetadb
... Dear https://www.biostars.org/u/287/, I would like to work on the count tables of normal and metastatic samples of Colon (Colorectal) cancer using RNA-seq. I tried this code from GEOmetadb but I did not get all the information. Do you think is there anyway I can address all the data that I want like ...
geometadb geo geoquery sradb rna-seq written 7 weeks ago by rahel1435020 • updated 7 weeks ago by Sean Davis25k
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
... Many thanks for your reply. Now it is more clear for me why I have such an output. ...
written 3 months ago by rahel1435020
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Comment: C: Differentially methylated regions (DMRs) and sites (DMCs) are not in the same re
... Thanks a lot for your reply. I was running all different packages and having the same result, now it is clear for me. ...
written 3 months ago by rahel1435020
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Differentially methylated regions (DMRs) and sites (DMCs) are not in the same region
... Dear all, I have some RRBS data with very low coverage and high number of NAs which they are aligned with BSMAP (more than 900,000 rows contain NAs). I did try many different packages but in all of them the DMRs and DMcs are completely different for example if gene A is detected as significantly me ...
metilene rrbs rnbeads methylkit written 3 months ago by rahel1435020 • updated 3 months ago by Devon Ryan84k
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Comment: C: error in using LOLA enrichment analysis in RnBeads
... I changed the version and unfortunately, I still have the same error! ...
written 4 months ago by rahel1435020
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Comment: C: error in using LOLA enrichment analysis in RnBeads
... sorry, edited now! even now I still have the error! ...
written 4 months ago by rahel1435020
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Comment: C: error in using LOLA enrichment analysis in RnBeads
... Here is: > sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1 ...
written 4 months ago by rahel1435020
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Comment: C: error in using LOLA enrichment analysis in RnBeads
... Many thanks for your prompt reply. The last version is 1.12.1 and I have the same Error there as well. I also have LOLA installed and included that one too (require(LOLA)) but still the same error is happening. ...
written 4 months ago by rahel1435020
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Comment: C: error in using LOLA enrichment analysis in RnBeads
... I want to start RnBeads full pipeline and in the beginning with setting rnb.options, I have this error. Here is my options: >rnb.options( exploratory.intersample = FALSE, exploratory.region.profiles = NULL, differential.enrichment.go=T, differential.enric ...
written 4 months ago by rahel1435020 • updated 4 months ago by WouterDeCoster32k

Latest awards to rahel14350

Popular Question 27 days ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Plotting numbers of somatic substitutions per megabase (MB)
Scholar 13 months ago, created an answer that has been accepted. For A: RRBS data analysis using RnBeads give Scan() error

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