User: Lauma R

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Lauma R0
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Posts by Lauma R

<prev • 12 results • page 1 of 2 • next >
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ChipSeeker Flanking gene annotation
... Dear All,    I have been using ChipSeeker for a while now, but I am struggling with understanding how does the flanking gene feature in annotatePeak works.  First, are theses genes meant to flank the peak or the gene assigned to the peak.  Second, are the geneIDs entrez IDs Third, the number of ...
chipseeker written 10 months ago by Lauma R0
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DiffBind different read counts depending on dba.count scores specified
... After closer inspection I noticed that Reads and RPKM values for the same samples in dba.counts$peaks changes depending which score metric I use. I was not quite sure if it something that should be expected, If that is the case, than why? My code is: dba.count_NON_INF.Reads <- dba.count( peak. ...
diffbind written 14 months ago by Lauma R0
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DiffBind Change of Metadata once dba.counts have been called
... Hi,    Thank you for all support so far.  I was looking back at previous posts, but couldn't find any question , so I will ask:  Is it possible to change metadata associated with dba object after dba.counts call. I am trying to understand my principal components better, and for that I would need ...
diffbind. change of metadata written 15 months ago by Lauma R0 • updated 15 months ago by Rory Stark2.8k
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Combine separate dba objects into the one
... Dear All,    I am currently analyzing large data set and to speed up things I am going to use cluster.  I am working with DiffBind packadge and I will create a single GRanges object that will be used for dba.counts function to create few smaller binding matrixes, than combine them in one dba obje ...
diffbind written 15 months ago by Lauma R0 • updated 15 months ago by Rory Stark2.8k
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Comment: C: Binding matrix creation DiffBind after MACS2 peak call
...       Dear Rory,  Thank you for your replay.  MACS2  is set to  —nomodel.  We are working on ATACseq data and we went for these MACS2 parameters following the suggestion from other group which is working on the same type of data.            ...
written 16 months ago by Lauma R0
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Binding matrix creation DiffBind after MACS2 peak call
...   Hello, I was looking at previous posts about MACS2 peak files and read shift before DiffBind to match MACS2 settings. However, I am still a bit confused about right steps to take. This is my work strategy: 1)  MACS2 was used for peak enrichment, with —shift -25 and —extsize 50 (thus shift 25b f ...
diffbind macs2 written 16 months ago by Lauma R0 • updated 16 months ago by Rory Stark2.8k
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How to correctly set DESeq2 design
... Hello,  I analyzed my RNAseq data with DESeq2 and currently I am trying to use it for the differential accessability estimation for ATACseq data.  However, I am not sure If I have made right design. I am sorry if this question hawe been asked before.  I want to perform Diff Exp/ Diff Access betwe ...
deseq2 written 17 months ago by Lauma R0
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Comment: C: DESeq2 iterate as an alternative sizeFactor estimator
... [13] compiler_3.4.0          htmlTable_1.9           scales_0.5.0            checkmate_1.8.5         [17] stringr_1.2.0           digest_0.6.12           foreign_0.8-69          XVector_0.16.0          [21] base64enc_0.1-3         pkgconfig_2.0.1         htmltools_0.3.6         limma_3.32.10        ...
written 21 months ago by Lauma R0
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Comment: C: DESeq2 iterate as an alternative sizeFactor estimator
... > sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    [3] LC_MONETARY=English_United Kingdom.1252 ...
written 21 months ago by Lauma R0
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Comment: C: DESeq2 iterate as an alternative sizeFactor estimator
... > idx.Blood.CD19 <- rowSums(counts(Blood.CD19.iterate, normalize = TRUE) >= 10) >=6 > Blood.CD19.keep <- Blood.CD19.coding[idx.Blood.CD19, ] > nrow(Blood.CD19.keep) [1] 12804 > Blood.CD19.keep  <- estimateSizeFactors(Blood.CD19.keep)  using 'avgTxLength' from assays(dds), ...
written 21 months ago by Lauma R0

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