User: Tefina Paloma

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Tefina Paloma220
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Posts by Tefina Paloma

<prev • 22 results • page 2 of 3 • next >
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reverse complement or no reverse complemnt on biomaRt / biomart.org
... Dear list, having a look at the vegfc gene (located on the reverse strand) on the website of biomart and querying the 5utr and the flanking sequence yields the following: http://www.ensembl.org/Homo_sapiens/Transcript/Export?db=core;g=ENSG00 000150630;output=fasta;r=4:177604691-177713895;strand=fe ...
biomart written 10.1 years ago by Tefina Paloma220
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getSequence: difference between coding_gene_flankand 5utr
... Thanks a lot, now things are much more clear to me. Best, Tefina ...
written 10.2 years ago by Tefina Paloma220
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getSequence: difference between coding_gene_flank and 5utr
... Dear list, I do have a question regarding getSequence and the difference between the seqType "coding_gene_flank" and "5utr". As far as I understand, "coding_gene_flank" should contain the 5utr. Looking at an example: library(biomaR) ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensem ...
alignment written 10.2 years ago by Tefina Paloma220 • updated 10.2 years ago by Rhoda Kinsella660
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Answer: A: biomaRt vs biomart.org
... Sean Davis writes: > Do you mean that they are not the same sequence or that they align to the > genome with a gap? This UTR covers two exons, so your sequence should align > with a gap. > > Sean > As far as I understand, the sequences should align to each other perfectly. Is ...
written 10.2 years ago by Tefina Paloma220
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biomaRt vs biomart.org
... Dear list, I am trying to retrieve 5' flanking sequences and 5' utr for several genes. Doing this via biomart.org or, respectively, biomarRt yields different results. An example, I want to retrieve the 5' flanking sequences (3000 bases) plus the 5' utr for the gene with the EntrezID 23704. My R c ...
homo sapiens biomart written 10.2 years ago by Tefina Paloma220
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Answer: A: biomaRt vs biomart.org
... Sean Davis writes: > Do you mean that they are not the same sequence or that they align to the > genome with a gap? This UTR covers two exons, so your sequence should align > with a gap. > > Sean > If I put as query sequence the sequence from biomart.org, and as subject sequen ...
written 10.2 years ago by Tefina Paloma220
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Answer: A: biomaRt vs biomart.org
... Tefina Paloma writes: > Can it be related to the fact that biomaRt is using the dataset > hsapiens_gene_ensembl, version NCBI35 > and biomaRt.org is using the Homo Sapiens genes, GRCh37? > Just a little correction, the dataset hsapiens_gene_ensembl in biomaRt is version NCBI36 (not ...
written 10.2 years ago by Tefina Paloma220
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Answer: A: Repeated gene entries on Toptable by limma
... Hi, if your are working with affymetrix arrays, you might also consider a custom CDF. Custom CDFs just represent an alternative to the affymetrix cdf, more up-to-date and the probe mapping is based on e.g. refseq or ensemble IDs. As far as I know these CDFs do not contain double entries. best, Te ...
written 10.2 years ago by Tefina Paloma220
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Comment: C: Array Set - Multiple Testing Problem
... Hello, first of all, thanks for all the answers. Unfortunately I do not have information about the exact probes- behaviour. The library was in-house selected and surely does not represent an uniform-behaving set of genes (like in the example of the hgu133a and b chip) In my special case we are ta ...
written 10.2 years ago by Tefina Paloma220
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Comment: C: Array Set - Multiple Testing Problem
... To be able to fit the same model to all arrays, an additional between- array normalization would be necessary, so to make all the arrays really comparable and I don't want to over-normalize the data either..... therefore I just thought of an sensible p value adjustment 2009/9/11 Sean Davis > ...
written 10.2 years ago by Tefina Paloma220

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