User: Johnson, Franklin Theodore

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Posts by Johnson, Franklin Theodore

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Comment: C: PAIR files -- feature set table
... Dr. Carvalho, Thanks for the email. I'm insignificant, but you are truly a gentlemen, scholar and a brilliant Spainard. I hope to cite you and your efforts in my future publications. Very humbly, Franklin Johnson ________________________________________ From: Benilton Carvalho [beniltoncarvalho@gm ...
written 6.4 years ago by Johnson, Franklin Theodore140
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Comment: C: FeatureExpressionSet using list.files() in place of read.xysfiles()
... Dr. Carvalho, Sorry to get back to you first. According to previous posts, http://comments.gmane.org/gmane.science.b iology.informatics.conductor/35367 I think it the XYS file error above may be related to the pdInfoBuilder annotation package, pd.pdinfo.gpl11164.ndf.txt. I went back to make the bui ...
written 6.4 years ago by Johnson, Franklin Theodore140
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Comment: C: FeatureExpressionSet using list.files() in place of read.xysfiles()
... Dr. Carvalho, Sorry that was my fault. Yea. I tried that way at first. But got the message below. > rawData=read.xysfiles(filelist, pkgname="pd.pdinfo.gpl11164.ndf.txt") All the XYS files must be of the same type. Error: checkChipTypes(filenames, verbose, "nimblegen") is not TRUE The logical for ...
written 6.4 years ago by Johnson, Franklin Theodore140
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FeatureExpressionSet using list.files() in place of read.xysfiles()
... Dear Dr. Carvalho, Thanks for the reply. I saw the thread of FAQs how to read in the annotation package made using pdInfoBuilder. For anyone having issues, it seems as straight forward as: #install pdinfo.gpl11164.ndf.txt install.packages("pd.pdinfo.gpl11164.ndf.txt", type="source", repos=NULL) Ins ...
microarray annotation go organism probe annotate limma convert pdinfobuilder sva written 6.4 years ago by Johnson, Franklin Theodore140 • updated 6.4 years ago by Benilton Carvalho4.3k
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Comment: C: PAIR files -- feature set table
... Dr. Carvalho, Yes. I see what you mean. Switching the columns helped in the FeatureSet table loading inserted more that 2 rows: Inserting 198661 rows into table featureSet... OK However, the warning message did print again. Warning message: In is.na(ndfdata[["SIGNAL"]]) : is.na() applied to non- ...
written 6.4 years ago by Johnson, Franklin Theodore140
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Comment: C: PAIR files -- feature set table
... Dear Dr. Carvalho, Recently, we had cooresponence regaring makePDInfoPackage for an NimbleGen apple microarray. I was able to merge the ndf design and XYS files using PROBE_ID. As a reminder this is a custom array, and there are no SIGNAL==NAs for control probes. It seemed to work: > makePdInfoP ...
written 6.4 years ago by Johnson, Franklin Theodore140
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Comment: C: PAIR files -- feature set table
... Resending to bioconductor message thread: Dear Dr. Carvalho, Thanks for the response. As you suggested, I will look into the merge function using "Probe_ID". After reading in the data, I will start here: merge.datasets(dataset1, dataset2, by="key"). Best Regards, Franklin Great minds discuss ideas ...
written 6.5 years ago by Johnson, Franklin Theodore140
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Comment: C: PAIR files -- feature set table
... Dear Dr. Carvalho, Muchos grasias for the reply. Actually, this is what my .ndf file looks like: > head(ndf) PROBE_DESIGN_ID CONTAINER DESIGN_NOTE SELECTION_CRITERIA SEQ_ID 1 7552_0343_0009 Duplicate_1 2 7552_0345_0009 Duplicate_2 3 7552_0347_0009 Duplicate_1 4 7552_0349_0009 Duplicate_ ...
written 6.5 years ago by Johnson, Franklin Theodore140
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Comment: C: No $df.residual
... limma 8.3--Ingenious! ...
written 6.5 years ago by Johnson, Franklin Theodore140
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Comment: C: No $df.residual
... Awesome, thanks! Great minds discuss ideas. Average minds discuss events. Small minds discuss people. -Eleanor Roosevelt ________________________________________ From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [sdavis2@mail.nih.gov] Sent: Tuesday, May 07, 2013 5:30 PM To: ...
written 6.5 years ago by Johnson, Franklin Theodore140

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