User: maria.maqueda

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Posts by maria.maqueda

<prev • 6 results • page 1 of 1 • next >
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Comment: C: HuGene20st - lincRNA annotation
... Thanks Jim for your quick and explanatory answer! 1) Understood. Fully agree that most probably I will finally prioritized transcripts with no additional information rather than an ID. 2) Thanks for sharing your experience, it's some how....disturbing. So, my personal outcome is that I will have ...
written 4.3 years ago by maria.maqueda0
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HuGene20st - lincRNA annotation
... Hello all, My name is Maria Maqueda and I am working with some data from HuGene20st microarrays (at transcript cluster level). This is not the first time working with these arrays but it seems I am again struggling with the annotation. Mainly, I have two questions: 1) Regarding lincRNA annotation. ...
hugene20sttranscriptcluster.db lincrna annotation affymetrix microarrays hugene20st written 4.3 years ago by maria.maqueda0 • updated 4.3 years ago by James W. MacDonald51k
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Comment: C: SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hi Katja,   Yes, this helps! Many thanks for answering so quick! I am just smoothing the meth data. Let's see what I have! Thanks again, Cheers Maria       ...
written 4.4 years ago by maria.maqueda0
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Answer: A: SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hi again Katja,     Following your suggestion to limit the coverage as indicated in the BiSeq vignette, I obtained the following error message while executing limitCov function: ​ "Error in methReads(object)[indCov] <- as.integer(round(fraction * maxCov)) :   NAs are not allowed in subscripted ...
written 4.4 years ago by maria.maqueda0
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Comment: C: SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hi Katja, Many thanks for you quick answer! Yes, I saw the very high coverage filtering in the BiSeq filtering, thanks for referring. Cheers Maria           ...
written 4.4 years ago by maria.maqueda0
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SAAP-BS data analysis (RRBS) - BiSeq use and Coverage Histogram
... Hello all,    I am struggling with the DMR analysis of some RRBS data already processed with SAAP-BS program. I do not have the SAM/BAM files, just a merged csv file with the methylC, totalC and Ratio per sample and CpG site (around 2.5M).  I am new to this type of analysis (previously worked with ...
coverage biseq rrbs saap-bs written 4.4 years ago by maria.maqueda0

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