User: JunLVI

gravatar for JunLVI
JunLVI30
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30
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New User
Location:
Japan
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32 minutes ago
Joined:
1 year, 4 months ago
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h***************@126.com

Posts by JunLVI

<prev • 26 results • page 1 of 3 • next >
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Answer: A: Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between file
... I did not figure out how to using DESeqDataSetFromHTSeqCount to input my data into DESeq2,  but tried "DESeqDataSetFromMatrix", and it worked out, I put it here, in case someone met similar issue: source("https://bioconductor.org/biocLite.R") biocLite("Rsubread") library("Rsubread") # count the ...
written 2 days ago by JunLVI30
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Comment: C: Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between file
... @Michael Love, thank you for your suggestion. I am not so sure what " count files have different length" means: here is the size of the files as the out put of HTSeq count ( I assume those are count files),  and the inside of the files (only 4 rows are shown), if that gives you some ideas or I hav ...
written 2 days ago by JunLVI30
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Error in DESeqDataSetFromHTSeqCount: Gene IDs (first column) differ between files.
... Hi, I was trying to import the count result from HTSeq Count into DESeq2.  # inside of "HTSeq_Count_ChIPpeak_H3K27ac_geneX.csv" "Samplename", "countfile", "genotype", "compartment" "H3K27ac_WTCellB","ChIPpeakWTCellB","WT","CellB" "H3K27ac_geneXcKOCellA","ChIPpeakgeneXcKOCellA","geneXcKO","CellA" " ...
htseqcounts deseq2 chipseq written 4 days ago by JunLVI30
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GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
...   Hi, I was trying to trying counts reads mapped onto a bed file,  I checked the workflow of "DESeq2" ,  gtffile <- ("mm9genes.gtf") library("GenomicFeatures") (txdb <- makeTxDbFromGFF(gtffile, format="gtf", circ_seqs=character())) (ebg <- exonsBy(txdb, by="gene")) ...
summarizeoverlaps genomicalignments written 7 days ago by JunLVI30 • updated 6 days ago by James W. MacDonald42k
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Metagene: file import and aesthetic customization
...     Hi I was trying to perform a metagene analysis.  I think I have gotten the files ready : a bed files + n bam files (sorted)  my questions are somewhat naive: 1. how to import these file in order to perform analysis?  in the vignette : bam_files <- get_demo_bam_files() regions <- g ...
ggplot2 metagene R written 7 days ago by JunLVI30 • updated 7 days ago by Charles Joly Beauparlant150
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DiffBind:issue when trying to read peaksets
... Hi I was trying to use DiffBind to analysis my ChIP-seq data. Following the sample given by Vignette, I created my sample sheet ("my_samples_sheet.csv")like this:  "SampleID","Tissue","Factor","Condition","Treatment","Replicate","bamReads","ControlID","bamControl","Peaks","PeakCaller" "H3K27ac_Xc ...
diffbind written 16 days ago by JunLVI30 • updated 16 days ago by Rory Stark1.7k
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Comment: C: Meaning of "Contrast" in "DESeq2" & how to compare the results of the same celll
... Thank you very much, Michael. You let me know where my problem lies, both technical one in this specific case and overall one,  plus the solution, that is much more that I should expected from some one who has developed the package. Really appreciate! ...
written 29 days ago by JunLVI30
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Comment: C: Meaning of "Contrast" in "DESeq2" & how to compare the results of the same celll
...     Hi Michael, Thank you very much for your feedback. Yes, today when I tried to understand the meaning of every function, I realized that, as you pointed out, I just  plotted the genes with highest variance, which inevitably led to the results that  top gene list was dominated by the genes diffe ...
written 29 days ago by JunLVI30
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Comment: C: Meaning of "Contrast" in "DESeq2" & how to compare the results of the same celll
... "The top gene list should not be dominated by gene with different base levels unless you are extracting the wrong coefficient"  Based on your comments here, I wondered that I might messed up with my design. After checking the code I used as I pasted in my previous comment, I realized that there see ...
written 4 weeks ago by JunLVI30
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Comment: C: Meaning of "Contrast" in "DESeq2" & how to compare the results of the same celll
... ​ sampleTable <- read.csv("samples.csv",row.names=1) filenames <- paste0(sampleTable$samplename,".bam") library("Rsamtools") bamfiles <- BamFileList(filenames, yieldSize=2000000) gtffile <- ("mm10genes.gtf") library("GenomicFeatures") (txdb <- makeTxDbFromGFF(gtffile, format="gtf", ...
written 4 weeks ago by JunLVI30

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