User: Tefina Paloma

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Tefina Paloma220
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Posts by Tefina Paloma

<prev • 22 results • page 1 of 3 • next >
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Answer: A: batch effect confounded with condition
... I have 2 conditions (lets call them conditon A and B) with 3 biolog. replicates each in batch 1. Additionally, I have 2 other conditions (conditions C and D) with 3 biolog. replicates in batch 2. Questions of interest are: - diff. expr. genes between A vs B, and C vs D - this can be done via LIMMA ...
written 7.3 years ago by Tefina Paloma220
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Answer: A: batch effect confounded with condition
... Thanks for all your answers. I think I will pursue the following strategy: I will analyse each experiment separately. Contrasts within each experiment should be fine. (As batch 1 concerns only experiment 1 and batch 2 concerns only experiment 2). Any comparisons between experiments ( = comparisons ...
written 7.3 years ago by Tefina Paloma220
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batch effect confounded with condition
... Dear List, I have microrarray data where condition is completely confounded with a time batch effect. When doing a PCA on the RMA normalized data, the first principal component separates clearly the two batches. What option do I have when I still want to compare different conditions across batches ...
go limma written 7.3 years ago by Tefina Paloma220
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strand consistency with readAligned, coverage and transcriptsBy
... Hi, I have a question regarding consistency of strand. Although reading the documentation and several tutorials I am not totally sure if I have understood everything right. Lets say you read in a fastq file from bowtie with readAligned. x = readAligned("fastq-file", type = "Bowtie"). For each re ...
coverage written 7.8 years ago by Tefina Paloma220 • updated 7.8 years ago by Steve Lianoglou12k
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Answer: A: reverse complement or no reverse complemnt on biomaRt / biomart.org
... Thanks a lot for your quick help, I am really thankful, best, Tefina ...
written 9.7 years ago by Tefina Paloma220
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Answer: A: reverse complement or no reverse complemnt on biomaRt / biomart.org
... Hi, So, regardless if the gene is on the forward or on the reverse strand, the "start coordinates" for any kind of sequence are always lower than the "end coordinates". e.g. for Gene ENSG00000150630, Transcript ENST00000280193 and Exon ENSE00001153189 Start: 177,713,319 End: 177,713,895 So, if th ...
written 9.7 years ago by Tefina Paloma220
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Answer: A: reverse complement or no reverse complemnt on biomaRt / biomart.org
... Thanks a lot for your help, whit blat everything is really clear to me now. But indeed, a rather bad bug in the export wizard. Best, Tefina ...
written 9.7 years ago by Tefina Paloma220
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Answer: A: reverse complement or no reverse complemnt on biomaRt / biomart.org
... I apologize for giving such a vague description. If I go to the ensemble page, click on "Mine Ensembl with BioMart", chose as database ensembl 56, Homo Sapiens, GRCh37, filter by ENST00000280193, click on results, and then click on the ENST00000280193 which leads to the transcript summary of this ...
written 9.7 years ago by Tefina Paloma220
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Answer: A: reverse complement or no reverse complemnt on biomaRt / biomart.org
... James W. MacDonald writes: Hi, if I just export the sequence by using the "export data" button on the left hand side of the biomart page. I do not do this ususally, but I just wanted to compare the different possibilities of exporting the sequence to make sure that I always get the same sequenc ...
written 9.7 years ago by Tefina Paloma220
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reverse complement or no reverse complemnt on biomaRt / biomart.org
... James W. MacDonald writes: > > The flanking sequence isn't reverse complemented in R, it is reported > exactly as it is received from the Biomart server. > > I am a bit confused here as well; AFAICT, the sequence for the 5' flank > and UTR are identical from all sources (Ensembl ...
biomart written 9.7 years ago by Tefina Paloma220

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