User: emmak

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emmak20
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5 months, 3 weeks ago
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7 months, 3 weeks ago
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Posts by emmak

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biomart R code cannot retrieve gene symbol
... Could you please let me know what I miss in this code ? It couldn't retrieve the symbol for ENSG00000275038, while the web interface returned AC091980.2. It works for most of genes but returns NA for a few genes.  Thanks for your help! ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl ...
biomart ensemble mart ensemblbiomart written 5 months ago by emmak20
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Comment: C: Correct version of EnsDb.Hsapiens for ensembl transcriptome
... Thank Mike, how about the error ? Do you see anything wrong ?   ...
written 7 months ago by emmak20
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Comment: C: Correct version of EnsDb.Hsapiens for ensembl transcriptome
... Thank you, Johannes! ...
written 7 months ago by emmak20
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Comment: C: Correct version of EnsDb.Hsapiens for ensembl transcriptome
... Thank Mike, I will go with ignoreTxVersion.  I tried to download hg38 transcriptome from ucsc (for salmon) but I am not sure which is correct one (please advise ). So, I tried mrna and refMrna (from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) but I got the above error for both. It look ...
written 7 months ago by emmak20
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Comment: C: Correct version of EnsDb.Hsapiens for ensembl transcriptome
... Thank you, Mike. I just added additional information. It ran if I used the ignoreTxVersion. But I worry that I may miss some genes because of the mismatch. ...
written 7 months ago by emmak20
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Correct version of EnsDb.Hsapiens for ensembl transcriptome
... I downloaded the transcriptome:  ftp://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz , to quantify read counts using Salmon. I thought it is equivalent to EnsDb.Hsapiens.v86, and created a data frame to map transcript id to gene id.  txdf <- transcri ...
rnaseq salmon ensembl release ensembldb tximport written 7 months ago by emmak20
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Comment: C: DESeq2 batch effect modeling and matrix not full rank
... Thank Mike!  it's a really clever trick.  ...
written 7 months ago by emmak20
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DESeq2 batch effect modeling and matrix not full rank
... Hi, I am trying to model batch effect with DEseq2 but get  "Error in checkFullRank(modelMatrix) : the model matrix is not full rank". My design formula is ~ BATCH + group. Basically, I want to find gene expressed differently between different groups. I don't see the linear dependent between BATCH a ...
rnaseq deseq2 rna-seq written 7 months ago by emmak20 • updated 7 months ago by Michael Love19k

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