User: jgarces

gravatar for jgarces
jgarces20
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20
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New User
Location:
Spain
Website:
https://github.com/jga...
Last seen:
1 week ago
Joined:
2 years, 8 months ago
Email:
j******@unav.es

Posts by jgarces

<prev • 25 results • page 1 of 3 • next >
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Answer: A: clusterProfiler::enrichGO() is getting very slow
... I faceted the same issue and I ran out of patience... maybe [enrichR][1] could helps you. Bests! [1]: https://cran.r-project.org/web/packages/enrichR/vignettes/enrichR.html ...
written 3 months ago by jgarces20
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Comment: C: Weird MA-plot (DESeq2)
... Thanks for your attention @geek_y. Yes, indeed, it'd be the way you point out... it was an typo error. ...
written 6 months ago by jgarces20
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Comment: C: Weird MA-plot (DESeq2)
... Thanks for your help, @ATpoint. Indeed, the problem was the very (excessive) variation in the number of raw counts. I tested only those samples between Q2 and Q3 (of `colSums(raw_counts)`) and I got an usual MA-plot... so the _easiest_ solution will be resequencing and balance all raw counts. So, th ...
written 6 months ago by jgarces20
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Comment: C: Weird MA-plot (DESeq2)
... Hi, @ATpoint. I'm comparing, in the same patient (eg, 341; within a big patients group), two different conditions (SP and MO)... at processed at the same time and following a 3`-RNAseq protocol. I wouldn't expect a very big difference but a bit... is this affecting the MA-plot? Thanks! ...
written 6 months ago by jgarces20
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Weird MA-plot (DESeq2)
... Hi, I'm running a RNAseq experiment comparing two different conditions on the same subject... my count matrix is some like that (but much bigger): 341_MO_r150 341_SP_r150 345_MO_r129 345_SP_r129 350_MO_r178 350_SP_r178 A1BG 0 0 2 0 ...
confounders deseq2 rna-seq written 6 months ago by jgarces20 • updated 6 months ago by geek_y11k
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Comment: C: Multiple N bases in RNAseq
... Thanks for your quick reply, @genomax. (yes, indeed, I'd want to say QC in the code I showed, already edited). I've reviewed all Illumina QCs in the sequencer and "Per tile sequence quality" and there's nothing related (in appearance) with the run's quality... I forgot to mention that is a generaliz ...
written 9 months ago by jgarces20
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Multiple N bases in RNAseq
... Hi there, I've recently sequenced some samples following a 3'-end RNA-seq protocol. When I watched FASTQs, I realized that multiple reads have Ns (in allmost all processed samples). Initially, I thought in the sample's quality (because I'm using very low amount of cells as input) or in a low diver ...
illumina rna-seq written 9 months ago by jgarces20
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Comment: C: PyClone without copy number data
... Hi @fongchunchan. I'm trying to extract minor and mayor cn info from sciClone but I'm not able to differentiate that value correspond to each one because this R package only give me an unique value of cn not two, could you help me? chr st 799_D.ref 799_D.var 799_D.vaf 799_D.cn 799_D. ...
written 16 months ago by jgarces20
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Activator o repressor protein in a pathway
... Hi there, Maybe it's a very basic question but I've surfed the (almost entire) web without any success... Once you've performed an functional enrichment (either ORA or GSEA) and detected key GOs or pathways implied in your disease, how can you know if a specific gene within a specific GO has a act ...
pathway written 16 months ago by jgarces20
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Comment: C: GISTIC2, some missing samples during the process
... Hi Kevin, you're right with the defaults parameters... I missed the `-maxseg` one and some samples had more segments that the default value. Sorry for this silly error. Thanks a lot! ...
written 17 months ago by jgarces20

Latest awards to jgarces

Popular Question 6 months ago, created a question with more than 1,000 views. For Why different tSNE plot with Seurat and Monocle if they'r using the same R package?
Popular Question 23 months ago, created a question with more than 1,000 views. For Why different tSNE plot with Seurat and Monocle if they'r using the same R package?

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