User: jgarces

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Posts by jgarces

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Rawcopy copy number analysis
... Hi Moritz, I'll try to answer you with my (little) experience with `rawcopy` (and after some emails with the package's author, he's very kind): - The correct output, I guess you mean the segmentation output, is the *segments.txt* file (the other ones are for generating the different plots for th ...
written 4 days ago by jgarces0
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Comment: C: CDF file for Cytoscan arrays
... Thanks Kevin. I've downloaded the CDF file from the second link and I've move to the folder with the CELs but errors don't disappear... thanks anyway! ...
written 17 days ago by jgarces0
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CDF file for Cytoscan arrays
... Hi there, I'm trying to read some CEL files from Cytoscan HD arrays with the R package `affy` but I get this (annoying) error: > u <- read.affybatch(filenames = list.files(pattern=".CEL$")) > u Error in getCdfInfo(object) : Could not obtain CDF environment, prob ...
array cystoscan cdf written 18 days ago by jgarces0
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Comment: C: cdf environment for cytoscan hd array
... Hi @arti.pandey69. Only for curiosity... how did you generate the `cychhp.txt` files? Manually through Affymetrix software or by another R package? Thanks a lot! ...
written 4 weeks ago by jgarces0
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Comment: C: How to find CNV or CN state information from rawcopy output ?
... Hi @lynn_redman, did the package's author answer you? ...
written 4 weeks ago by jgarces0
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(Closed) Extract genes around chromosomal position
... Hi there, I'm trying to extract the genes that are around a chromosomal position (let's talk about 1Kb up and downstream, for example), i.e.: taking account position chr1:46508903 see those genes that are 1Kb up and down. Does anybody know if there's a software/script/whatever that can help me to ...
genome chromosomal position written 4 months ago by jgarces0
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Comment: C: High Kmer Content in middle of the read
... Ok, thanks anyway... so I guess, according to Ian's response, that's useless try to do some kind of trimming, isn't it? Thanks again! ...
written 5 months ago by jgarces0
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Answer: A: High Kmer Content in middle of the read
... Hi @Sam, I've got exactly the same problem with my samples... can you finally solve it?? I'd expect that adapter contamination or mis-incorporation were in the 5'/3'-ends but I don't understand why it's appearing in the middle... Thanks a lot! ...
written 5 months ago by jgarces0
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Answer: A: Varscan2 copynumber 'Parsing Exception' error
... Hi there, I'm having the same issue with VarScan and I'm wondering if there's any option **not** to deactivate the BAQ option (`-B`) in `mpileup` (to calculate base alignment quality) and pipe it to VarScan somatic... if not, how much information about alignment is lost and it'd be relevant? Than ...
written 5 months ago by jgarces0
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Comment: C: Why different tSNE plot with Seurat and Monocle if they'r using the same R packa
... Thanks both, guys! Nothing simpler that set.seed()... ...
written 9 months ago by jgarces0

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Popular Question 4 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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