User: michael watson IAH-C

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Posts by michael watson IAH-C

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Comment: C: DESeq and number of replicates required for RNA-Seq
... Hi Naomi Thanks for the reply. The issue isn't necessarily low expressing genes, but perhaps high expressing genes with a small (ish) fold change. DESeq seems to only report as significant differences that are high fold changes. Contrast this to limma for microarrays, where small fold changes ca ...
written 9.1 years ago by michael watson IAH-C3.4k
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DESeq and number of replicates required for RNA-Seq
... Hi This follows on slightly from my experimental design thread. Having worked through the vignette for DESeq, it seems to work well. However, for the TagSeqExample.tab data set, when using an FDR cut off of 0.05, what we see is that we only find differential expression for large fold changes - an ...
go deseq written 9.1 years ago by michael watson IAH-C3.4k • updated 9.1 years ago by Naomi Altman6.0k
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Comment: C: Experimental design for RNA-Seq
... Jakob An excellent answer, thank you. You say each sample has been sequenced four times due to the 12-plexing. What kind of variation do you see for the counts across those four times? Thanks Mick ________________________________________ From: Jakob Hedegaard [Jakob.Hedegaard@agrsci.dk] Sent: 30 ...
written 9.1 years ago by michael watson IAH-C3.4k
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Answer: A: R: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... Hi I parsed your entire ID list and used it in the same code I produced below, and it worked. My id list was a vector - I wonder if your construct genes_map[,"ensembl_transcript_id"] produces not a vector, but a factor, which may cause problems for biomaRt? I'm just guessing though. Bioc package ...
written 9.1 years ago by michael watson IAH-C3.4k
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Answer: A: why biomaRt cannot extract 3UTR sequences for 1941 ENSGxxxxx ?
... The following (small) code works for me: library(biomaRt) mart <- useMart("ensembl","hsapiens_gene_ensembl") ids <- c("ENST00000262187","ENST00000296271") seq <- getSequence(id=ids, type="ensembl_transcript_id", mart=mart, seqType="3utr") seq ________________________________________ From: ...
written 9.2 years ago by michael watson IAH-C3.4k
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Comment: C: Experimental design for RNA-Seq
... Great stuff, thanks Steve and Naomi. I guess I was thinking of technical replicates simply as sequencing the same library on multiple occasions; though creating two libraries out of one sample adds an extra layer of complexity. What is the evidence (if any) that lane and/or library preparation ca ...
written 9.2 years ago by michael watson IAH-C3.4k
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Experimental design for RNA-Seq
... Dear List I'm about to design a simple experiment (knockout vs wild-type) and we plan to use RNA-Seq. We're interested in gene expression, for mRNA and microRNAs in particular, and calculating stats for differential expression. I'm aware of DEseq, DEGseq and edgeR. I wanted to ask those who have ...
edger degseq deseq written 9.2 years ago by michael watson IAH-C3.4k • updated 9.2 years ago by Naomi Altman6.0k
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Comment: C: Human, Mouse and Rat homologs
... Lets say your data is in a data frame called "d", then the code might be: > d probe_id ensembl_id 1 8039748 ENSG00000121410 2 7960947 ENSG00000175899 3 8144857 ENSG00000171428 4 8144866 ENSG00000156006 5 7976496 ENSG00000196136 6 8083415 ENSG00000114771 > > library(biomaRt) & ...
written 9.2 years ago by michael watson IAH-C3.4k
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GEOquery: invalid class "ExpressionSet" object: featureNames differ between assayData and featureData
... Hi Setting aside the obvious problems with the NCBI ftp site at present..... I manually downloaded a series matrix file, GSE6198_series_matrix.txt.gz and I have two questions: Firstly, why am I getting these errors: > geo <- getGEO(file="GSE6198_series_matrix.txt.gz", GSEMatrix=TRUE) File ...
written 9.2 years ago by michael watson IAH-C3.4k
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Answer: A: R: Validated miRNAs revisited
... There's a couple of things of note here. Last time I looked, TarBase had about 1300 records and miRecords 1600. This data covers a number of species, across hundreds of microRNAs and 10000's of genes per species. The take home message is that these databases are hopelessly incomplete, and cover on ...
written 9.2 years ago by michael watson IAH-C3.4k

Latest awards to michael watson IAH-C

Popular Question 9.1 years ago, created a question with more than 1,000 views. For DESeq and number of replicates required for RNA-Seq
Popular Question 9.1 years ago, created a question with more than 1,000 views. For how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
Popular Question 9.1 years ago, created a question with more than 1,000 views. For biomaRt connection problems
Popular Question 9.1 years ago, created a question with more than 1,000 views. For How do I get p-values from multtest?
Popular Question 9.1 years ago, created a question with more than 1,000 views. For biomaRt connection problems
Centurion 9.1 years ago, created 100 posts.

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