User: ilyco

gravatar for ilyco
ilyco50
Reputation:
50
Status:
New User
Location:
United Kingdom
Last seen:
1 year, 10 months ago
Joined:
5 years, 3 months ago
Email:
i*********@gmail.com

Posts by ilyco

<prev • 24 results • page 1 of 3 • next >
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Comment: C: edgeR direction of expression and sign of Log Fold Changes
... There are 6 conditions in the experiment and one is the baseline. Why should I swap the labels? ...
written 3.2 years ago by ilyco50
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edgeR direction of expression and sign of Log Fold Changes
... Hi, I used edgeR for differential expression analysis with 5 conditions relative to the baseline condition. The design was a simple linear model with the condition factor variable re-ordered so that the baseline is the first value. The code was the following: design <- model.matrix(~ con ...
R rna-seq edger lfc written 3.2 years ago by ilyco50 • updated 3.2 years ago by Gordon Smyth980
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Comment: C: BAM file header after splitting paired end reads
... Thank you very much. I used -b and made sure it is a BAM file. Even so, it still would not let me read the file and output "malformatted header".  I then used samtools reheader and removed chromosome fragments e.g. chr_Un from the header.  HiFive still does not recognise the pair of reads and outp ...
written 3.6 years ago by ilyco50
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BAM file header after splitting paired end reads
... Hi, I am processing BAM files using pysam as part of the HiFive set of tools for analysing Hi-C data. The input required are two BAM files with each one representing the forward and the reverse reads respectively from an alignment of paired-end reads.  In order to split the alignment BAM file into ...
samtools paired-end bam hifive sam written 3.6 years ago by ilyco50 • updated 3.6 years ago by Pierre Lindenbaum122k
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Comment: C: How to create Hi-C analysis package HiFive fend object
... Hi, I took the digested genome file from hicup and extracted the fields for chr start end. Then added the following columns:  name score strand gc and mappability. name score and strand each had only "." elements and gc and mappability have only "0,0" elements. I then ran hifive fends -B testfends. ...
written 3.6 years ago by ilyco50
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Comment: C: DESeq2 and edgeR - no agreement between results
... Here is a summary of the results with DESeq2: > summary(res) out of 15630 with nonzero total read count adjusted p-value < 0.01 LFC > 0 (up) : 2076, 13% LFC < 0 (down) : 1660, 11% outliers [1] : 1368, 8.8% low counts [2] : 1366, 8.7% (mean count < 2) [1] see 'cooksCu ...
written 3.8 years ago by ilyco50
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Comment: C: DESeq2 and edgeR - no agreement between results
... Thank you for the suggestion. It helped a lot to choose only one condition and check every step. The "normalised" counts correlate very well but logFC still correlates poorly between edgeR and DESeq2 for each condition. ...
written 3.8 years ago by ilyco50
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Comment: C: DESeq2 and edgeR - no agreement between results
... I applied a cutoff for the adjusted pvalue of 0.01. The different logFC values are for all the genes not just the differentially expressed ones. I ran the typical: dds <- dds[ rowSums(counts(dds)) > 1, ] dds <- DESeq(dds) res <- results(dds) in DESeq2  and the typical: y <- DGEL ...
written 3.8 years ago by ilyco50
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Comment: C: DESeq2 and edgeR - no agreement between results
... Some difference is indeed to be expected but a negative correlation between logFC changes and only a 20% match in results seems a bit over the top. I am looking for potential causes. The code is rather long and does not use anything new. I simply copy pasted the typical commands from the vignettes o ...
written 3.8 years ago by ilyco50
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Comment: C: DESeq2 and edgeR - no agreement between results
... In each case, DESeq2 calls about 2000 genes and edgeR about 1000-1400. I checked the correlation between the logFC in DESeq2 and edgeR and it is very bad in every case. For one condition, it even correlates negatively. I am not sure why.  ...
written 3.8 years ago by ilyco50

Latest awards to ilyco

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For JASPAR, TFs and their target genes

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