User: Andrea Grilli

gravatar for Andrea Grilli
Andrea Grilli240
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240
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Location:
Italy, Bologna, Rizzoli Orthopaedic Institute
Website:
http://www.ior.it/rice...
Last seen:
4 years, 2 months ago
Joined:
8 years, 3 months ago
Email:
a************@ior.it

Posts by Andrea Grilli

<prev • 28 results • page 1 of 3 • next >
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Comment: C: DEXSeq: 0 reads for all exons for an expressed gene
... Hi Alejandro, sorry for the late reply but I was waiting the answer from the facility who did the alignment. - The aligner is TopHat/Bowtie with default settings - Indeed, if I correctly interpret the output, reads are mapping to two different regions. Checking in SAMPLE 1 the first read from previo ...
written 4.3 years ago by Andrea Grilli240
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Comment: C: DEXSeq: 0 reads for all exons for an expressed gene
... Hi Alejandro, thank you for your quick reply. I'm sorry but I haven't sam files of my samples but bam only, so I can have index only for position-sorted files.   I'm not sure if following step could be a proper method, but I tried sorting by bash command the output of the bam files indexed by pos ...
written 4.3 years ago by Andrea Grilli240
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DEXSeq: 0 reads for all exons for an expressed gene
... Dear Mailing list, I'm using DEXSeq to analyze RNA-seq data from Illumina HiSeq2000 sequencer. I followed all the steps according to the vignette, getting a count of reads at exon level / per gene / per sample. Next steps into R work perfectly. Anyway, I have some problem with the upstream passage ...
dexseq written 4.3 years ago by Andrea Grilli240
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summarization for G4110B two colors agilent array: how to?
... Dear BioC list, I'm analyzing for the first time old data from Agilent two colors arrays (array version G4110B). As experimental design, I have 3 time points x 2 replicates at each time point in a treated vs control experiment. Arrays were hybridized at 2 different times, so I decided to reduce an ...
twochannel normalization limma marray agilent written 4.7 years ago by Andrea Grilli240 • updated 4.7 years ago by Gordon Smyth38k
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affy plus2 array - unclear probeset signal
... Dear BioC members, we profiled a cell line (parental) in a time-series experiment, comparing it with the same cell line transfected by a gene. We verified the transfection by real-time PCR and it was ok. When we moved to gene profiling (HG-U133a plus2 array), I discovered that the 2 probesets matchi ...
probe inversion written 6.3 years ago by Andrea Grilli240
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Comment: C: retrieve expression of all probes in the probe set
... Thanks Jim, now is clearer and the code works perfectly, Andrea Quoting "James W. MacDonald" : > Hi Andrea, > > On 10/15/2012 11:01 AM, andrea.grilli at ior.it wrote: >> Dear BioC list, >> I'm performing an analysis with Gene Chip hgu133a plus 2.0 array in >> two differe ...
written 6.9 years ago by Andrea Grilli240
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retrieve expression of all probes in the probe set
... Dear BioC list, I'm performing an analysis with Gene Chip hgu133a plus 2.0 array in two different cell lines. I'm interested in the expression of a specific gene and two different probesets match it: despite one is saying no difference exists, the other is suggesting a strong down-regulation. Checki ...
hgu133a probe written 6.9 years ago by Andrea Grilli240 • updated 6.9 years ago by James W. MacDonald51k
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Comment: C: outlier probes detection
... Yes, now I notice that point. Thank you so much for your help, Andrea "Hooiveld, Guido" ha scritto: > Hi Andrea, > I have to admit that it has been a while since I actively used > Harshlight. However, AFAIK Harshligt detect both outlier probes. You > can have Harslight automatically ...
written 7.4 years ago by Andrea Grilli240
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Comment: C: outlier probes detection
... Hi Guido, thank you for your reply. I checked the package Harshlight you suggested. Although it detects outlier arrays (and not outlier probes) it works well for the case, because it gives a percentage of the defects and that's better than a simple visual evaluation. I have one question about the pa ...
written 7.4 years ago by Andrea Grilli240
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outlier probes detection
... Dear all, I'm performing an analysis on HGU133plus2 arrays with 40 samples; looking at their surface with "affyPLM" package, I've seen a couple of arrays with small scratches and one more with a small bubble. Because I don't want to exclude these arrays (according to Murphys' law 2 on 3 belong to t ...
hgu133plus2 written 7.4 years ago by Andrea Grilli240 • updated 7.4 years ago by Djork Clevert210

Latest awards to Andrea Grilli

Popular Question 4.2 years ago, created a question with more than 1,000 views. For summarization for G4110B two colors agilent array: how to?
Popular Question 4.2 years ago, created a question with more than 1,000 views. For DEXSeq: 0 reads for all exons for an expressed gene

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