User: ZheFrench

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ZheFrench210
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210
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Location:
France
Last seen:
3 days ago
Joined:
3 years, 11 months ago
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Posts by ZheFrench

<prev • 55 results • page 1 of 6 • next >
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Answer: A: How to convert log2FC (Fold Change) obtained by differential expression analysis
... Function I use, where base = 2 def logratio2foldchange (logratio, base) : retval = base^(logratio) if retval < 1 : return -1/retval else : return retval ...
written 14 days ago by ZheFrench210
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Normalise batch effects for Percent Spliced In (PSI) matrice
... The exon-inclusion ratio, also known as percent spliced in (PSI), is a popular statistic for measuring alternative splicing events. How do you correct batch effects for matrice with this kind of values ? For gene expression, you can use combat or sva, but for psi (value between -1;1) ? Any ideas ...
sva combat splicing written 9 weeks ago by ZheFrench210
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FastQ ColorSpace to BaseSpace format in 2018
... Nowadays, is there a good way to convert colorSpace fastq from ABI platform to base space format ? Or at least, to align them in bam and maybe then you can extract to base space fastq ... I'm used to work with STAR for alignment but it's not designed to align colorspace fastq(same for bowtie2)...s ...
colorbase written 4 months ago by ZheFrench210 • updated 4 months ago by h.mon24k
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How to visualise/explore Hi-C maps per chromosome at 100Kb and 40Kb
... From here[enter link description here][1] I can download Hic maps per chromosome at 100kb and 40 kb . I have no expertise with Hic data. I was wondering how to exploit these files which extension is ."abc". I'd like to have coordinates in text file with regions of interaction and strength/statistics ...
hic written 4 months ago by ZheFrench210 • updated 4 months ago by Alex Reynolds27k
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BSgenome.Hsapiens.UCSC.hg38 vs BSgenome.Hsapiens.NCBI.GRCh38
... I am wondering what is the difference between this two reference package in R ? hg38 and GRCh38 should be same sequence assembly, right ? So what the point of creating this two reference package to access raw sequence. ...
genome R version assembly written 5 months ago by ZheFrench210 • updated 5 months ago by igor7.4k
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Comment: C: DESEQ2 size factors change when number of samples change in the design
... Ok I got it , but do you know how is it computed ? ...
written 6 months ago by ZheFrench210
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DESEQ2 size factors change when number of samples change in the design
... For example, when you analyse Untreated condition vs Day1Treatment condition with only these samples in your design you will get some size factors. If you have also set up a Day6Treatment condition in your design (but you don't use it yet), and want to to do the same comparison Untreated vs Day1Tre ...
deseq2 written 6 months ago by ZheFrench210 • updated 4 months ago by erwan.scaon640
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Heatmap with normalised count from DESEQ2
... I was wondering which is better (or if one of this method is wrong ) for plotting in a heatmap normalised count from deseq2 : `counts(dds,normalized=TRUE)` : z-score( log2(norm count +1) ), z-score(norm count ) or just log2(norm count +1) ...
deseq2 heatmap written 6 months ago by ZheFrench210 • updated 6 months ago by Kristin Muench380
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Comment: C: How to define Basal B subtype from TCGA breast cancer patient samples ?
... Yeah that was my first idea. By the way how do you scaled TPM values ? ...
written 7 months ago by ZheFrench210
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How to define Basal B subtype from TCGA breast cancer patient samples ?
... TCGA provide a molecular classification (Luminal A , Luminal B, Basal, Normal like, HER2 enriched) Basal subtype can be divided in basal A and basal B. (Kao et al., 2009; Neve et al., 2006) It has been done using expression from MicroArray via Significance Analysis of Microarrays (SAM) or PAM using ...
tcga cancer written 7 months ago by ZheFrench210

Latest awards to ZheFrench

Popular Question 26 days ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Great Question 5 weeks ago, created a question with more than 5,000 views. For Trimming TruSeq Universal Adapter (Trimmomatic)
Student 9 weeks ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 3 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 6 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 7 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Popular Question 10 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
Student 13 months ago, asked a question with at least 3 up-votes. For Trimming TruSeq Universal Adapter (Trimmomatic)
Popular Question 13 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
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Popular Question 20 months ago, created a question with more than 1,000 views. For Snpsift extractFields : How Fields Annotation ANN[*].XX is working ?
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Popular Question 2.1 years ago, created a question with more than 1,000 views. For Samtools tview : what does underlined reads mean ? Secondary or Orphan

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