User: Jason

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Jason20
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1 year, 8 months ago
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4 years, 10 months ago
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Posts by Jason

<prev • 14 results • page 1 of 2 • next >
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Match read length and quality string length
... Hi, I trimmed the first 9 bases of my paired-end RNAseq fastq files and compared the results using FastQC with pre-trimmed *.fastq(s). Now I am trying to align the files using MapSplice but the program terminates in the first check when it is "checking read format". **For some particular reads the ...
fastq rna-seq sequencing written 22 months ago by Jason20 • updated 10 days ago by peterhuang11080
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Pipeline For Hugene-1_0-St-V1 Analysis
... Hi, Could someone please suggest a tutorial/pipeline, preferably in R, for analysis of HuGene-1_0-st-v1. I have been searching all day and can't find a pipeline that will automate pre-processing to differential gene expression analysis for this array type. Thanks in advance, Jason ...
R affymetrix written 4.4 years ago by Jason20 • updated 4.4 years ago by Scott Beeler0
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Comment: C: Create A Tab-Delimited Annotation Table From Csv Annotation File
... Thanks a bunch! I'm sure its going to do the job. Still it would be great if you could tell how you did it. ...
written 4.5 years ago by Jason20
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Comment: C: Create A Tab-Delimited Annotation Table From Csv Annotation File
... You're right, the code is quite old. But then again I don't really have a lot of available solution or I'm probably not aware of. affxUrl() is a parameter to readAnnotation() which itself calls read.table implicitly. The help file states that the argument affxUrl() usually need not to be overwritte ...
written 4.5 years ago by Jason20
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Create A Tab-Delimited Annotation Table From Csv Annotation File
... Hi, I want to create an tab-delimited annotation table from an affymetrix SNP6 CSV annotation file. I don't want the extra lines from the CSV file apart from the annotation table present in the middle of the CSV file. I tried using "AffyCompatible" package but it downloads the latest "na" version ...
R affymetrix written 4.5 years ago by Jason20 • updated 4.5 years ago by Neilfws47k
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Comment: C: How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
... I checked the link you shared and that's only for writing raw values from dataset whereas I'm interested in writing the ouput of doCRMAv2 into a tab-delim file as above. ...
written 4.5 years ago by Jason20
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Comment: C: How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
... Thanks a lot. Could you also tell how to use doCRMAv2 using a additional .CEL files/dataset as reference? I have checked its help file and I can't find a way to add external dataset as reference. ...
written 4.5 years ago by Jason20
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Comment: C: How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
... Case-median of all cases. I went through the website the whole day and somehow always ended up on the "Write a tab-delimited UGP" an related link which give incomplete information on the problem. Somehow, this page never showed up. One of those days I guess. Thanks a lot, I will try this too. ...
written 4.5 years ago by Jason20
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How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
... Hi, I have checked the whole aroma.affymetrix website but I can't seem to work out their tutorials on creating a tab-delimited text file from doCRMAv2() output. What I need is a table with following columns Each sample contains the LogR. Any help would be a appreciated!! Thanks Jason ...
R affymetrix written 4.5 years ago by Jason20 • updated 4.5 years ago by Irsan6.6k
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Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format
... Hi everyone, I am looking for a tool to convert Affy OncoScan format files into Affy SNP6.0 files. Affy 6.0 SNP array file is a cumulative file of LogR for all samples whereas Affy OncoScan provide individual file for LogR for each sample. I believe it can be done with a code in any suitable progr ...
R tools written 4.5 years ago by Jason20

Latest awards to Jason

Popular Question 4.0 years ago, created a question with more than 1,000 views. For How To Create Tab-Delimited Copy Number Files From Aroma.Affymetrix Output
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Pipeline For Hugene-1_0-St-V1 Analysis
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Create A Tab-Delimited Annotation Table From Csv Annotation File
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Rename Files In Subfolders In R

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