User: hrishi27n

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hrishi27n0
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Posts by hrishi27n

<prev • 14 results • page 1 of 2 • next >
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Comment: C: sc-RNA data analysis using scater
... Aaron, Thanks for the reply. My "read count" file does't include the ERCC's. A grep for "^ERCC-" doesn't really give anything, however the ERCC's are provided in a separate file. I guess I might have to do a rbind on the gene count file to include the spike-in data.  ...
written 7 weeks ago by hrishi27n0
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champ.load getting filtered RGChannelSet
... Hello, I am using champ.load to filter my probes from my IDAT files. I understand the champ.load function returns mset,rgset,pd,beta etc. I see that the mset includes the filtered features(everything left after det P,dropSNP,dropXY), but the rgset is unchanged, I have pasted a section of the output ...
champ methylation written 7 weeks ago by hrishi27n0 • updated 16 days ago by Yuan Tian40
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sc-RNA data analysis using scater
... Hello All, I am trying to analyze data for a single cell RNA sequencing experiment, for QC and normalization I am considering using the scater package. There are a few things I would like to know before starting analyzing this dataset. All your help and suggestions are much appreciated. This is my ...
scater scrna written 7 weeks ago by hrishi27n0 • updated 7 weeks ago by Aaron Lun14k
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Comment: C: Scran normalization error with computeSumFactors
... Thanks for the reply Aaron. I will try reducing the pool sizes, you are also right that I need an aggressive filtering strategy. I will add something like below to ensure that lowly expressed genes are removed.   keep_feature <- rowMeans(counts(ScaterObject)) >= 5 ...
written 7 weeks ago by hrishi27n0
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Scran normalization error with computeSumFactors
... Hello All, I am trying to analyze sc-RNA data using both scater and scran. While trying to run normalization using scran via the computeSumFactors method, I get the following error. Could someone please explain me what this error means and if there a way to fix it? Appreciate all your help and sugg ...
scran scater written 7 weeks ago by hrishi27n0 • updated 7 weeks ago by Aaron Lun14k
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Answer: A: Error using Bumphunter and Block finder using CHAMP
... Thanks for replying.  You are right about the message with "0 clusters", I was using only 10 CpG's for my test run, using all CpG's solved the problem. ...
written 3 months ago by hrishi27n0
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Error using Bumphunter and Block finder using CHAMP
... Hello, I am using ChAMP for my methylation analysis. In my case my data isn't normalized through the ChAMP pipeline. I am hoping to use ChAMP from section 5.6 of the tutorial.(https://bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html) I was able to run DMP successfully but ...
champ methylation 450k written 3 months ago by hrishi27n0
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Error while using ChAMP
... Hello All, I am using ChAMP do run a methylation analysis on the 450k dataset. I am not running every step individually but using the champ.process function to run the entire pipeline just by providing location to my IDAT directory which has my the sample_sheet.csv file. The program does run for a ...
champ methylation illuminahumanmethylation450k.db illumina450k written 4 months ago by hrishi27n0 • updated 4 months ago by Yuan Tian40
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Comment: C: dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : repla
... Hey, did you ever get an fix for the error? I am using the most recent version (the one mentioned above) and stuck with the same error.  ...
written 4 months ago by hrishi27n0
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Creating a GenomicRatioSet with non minfi normalized data
... I have methylation data that is pre-processed and normalized with an unpublished normalization method, I am hoping to run DMR and DMP analysis on this dataset using minfi. Currently, I have Beta values, M-values, P-values and pData(sample_info, age,sex etc), I am trying to create the GenomicRatioSet ...
minfi methylation illumina450k written 4 months ago by hrishi27n0

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